dbSNP rs3828357: ENSG00000291096:n.711A>G (chr3-125929513-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000340333.8(ENSG00000291096):n.711A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.358 in 1,596,110 control chromosomes in the GnomAD database, including 104,343 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 8870 hom., cov: 32)

Exomes 𝑓: 0.36 ( 95473 hom. )

Consequence

ENSG00000291096
ENST00000340333.8 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.93

Publications

18 publications found

Variant links:

Genes affected

ENSG00000291096 (HGNC:):

ENSG00000291096 links:

ALG1L1P (HGNC:33721): (ALG1 like 1, pseudogene) Predicted to enable mannosyltransferase activity. Predicted to be involved in protein glycosylation. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ALG1L1P links:

FAM86JP (HGNC:44097): (family with sequence similarity 86 member J, pseudogene)

FAM86JP links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000340333.8, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.013293445).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000340333.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
FAM86JP	NR_024250.1	n.1432T>C	non_coding_transcript_exon	Exon 5 of 5
FAM86JP	NR_024251.1	n.1530T>C	non_coding_transcript_exon	Exon 5 of 5
ALG1L1P	NR_171194.1	n.818A>G	non_coding_transcript_exon	Exon 7 of 7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000291096	ENST00000340333.8	TSL:1	n.711A>G	non_coding_transcript_exon	Exon 6 of 6
FAM86JP	ENST00000467239.6	TSL:1	n.1484T>C	non_coding_transcript_exon	Exon 5 of 5
FAM86JP	ENST00000485843.4	TSL:1	n.1654T>C	non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50864

AN:

151892

Hom.:

8873

Cov.:

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.450

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.276

Gnomad FIN

AF:

0.436

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.335

GnomAD2 exomes

AF:

0.336

AC:

78478

AN:

233450

AF XY:

0.341

show subpopulations

Gnomad AFR exome

AF:

0.262

Gnomad AMR exome

AF:

0.234

Gnomad ASJ exome

AF:

0.448

Gnomad EAS exome

AF:

0.280

Gnomad FIN exome

AF:

0.429

Gnomad NFE exome

AF:

0.382

Gnomad OTH exome

AF:

0.357

GnomAD4 exome

AF:

0.360

AC:

520248

AN:

1444100

Hom.:

95473

Cov.:

AF XY:

0.360

AC XY:

258706

AN XY:

718794

show subpopulations

African (AFR)

AF:

0.258

AC:

8628

AN:

33402

American (AMR)

AF:

0.243

AC:

10854

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.451

AC:

11788

AN:

26132

East Asian (EAS)

AF:

0.277

AC:

11015

AN:

39694

South Asian (SAS)

AF:

0.280

AC:

24126

AN:

86164

European-Finnish (FIN)

AF:

0.418

AC:

15885

AN:

38032

Middle Eastern (MID)

AF:

0.393

AC:

1624

AN:

4134

European-Non Finnish (NFE)

AF:

0.373

AC:

415172

AN:

1111726

Other (OTH)

AF:

0.352

AC:

21156

AN:

60108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

23819

47638

71458

95277

119096

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12910

25820

38730

51640

64550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.335

AC:

50862

AN:

152010

Hom.:

8870

Cov.:

AF XY:

0.333

AC XY:

24723

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.264

AC:

10946

AN:

41482

American (AMR)

AF:

0.274

AC:

4186

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.450

AC:

1558

AN:

3464

East Asian (EAS)

AF:

0.275

AC:

1421

AN:

5162

South Asian (SAS)

AF:

0.276

AC:

1329

AN:

4810

European-Finnish (FIN)

AF:

0.436

AC:

4598

AN:

10538

Middle Eastern (MID)

AF:

0.337

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.378

AC:

25703

AN:

67944

Other (OTH)

AF:

0.334

AC:

705

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1757

3514

5272

7029

8786

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.360

Hom.:

3625

Bravo

AF:

0.321

Asia WGS

AF:

0.263

AC:

915

AN:

3478

EpiCase

AF:

0.379

EpiControl

AF:

0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.96

DEOGEN2

Benign

0.050

Eigen

Benign

-0.38

Eigen_PC

Benign

-0.43

FATHMM_MKL

Uncertain

0.89

LIST_S2

Benign

0.75

MetaRNN

Benign

0.013

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.7

PhyloP100

4.9

PrimateAI

Uncertain

0.74

PROVEAN

Uncertain

-2.9

REVEL

Benign

0.18

Sift

Benign

0.081

Sift4G

Uncertain

0.053

Varity_R

0.25

gMVP

0.57

Mutation Taster

=85/15

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over