dbSNP rs3138035: ENSG00000310445:n.141G>A (chr17-34318930-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000849825.1(ENSG00000310445):n.141G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,358 control chromosomes in the GnomAD database, including 6,739 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 0.27 ( 6726 hom., cov: 33)

Exomes 𝑓: 0.38 ( 13 hom. )

Consequence

ENSG00000310445
ENST00000849825.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.92

Publications

17 publications found

Variant links:

Genes affected

ENSG00000310445 (HGNC:):

ENSG00000310445 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310445	ENST00000849825.1 link	n.141G>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000310445	ENST00000849826.1 link	n.28G>A		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41600

AN:

152022

Hom.:

6726

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.287

Gnomad AMR

AF:

0.219

Gnomad ASJ

AF:

0.363

Gnomad EAS

AF:

0.0953

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.414

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.368

Gnomad OTH

AF:

0.274

GnomAD4 exome

AF:

0.375

AC:

AN:

216

Hom.:

AF XY:

0.331

AC XY:

AN XY:

118

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.355

AC:

AN:

138

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.405

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.273

AC:

41596

AN:

152142

Hom.:

6726

Cov.:

AF XY:

0.274

AC XY:

20383

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.121

AC:

5005

AN:

41534

American (AMR)

AF:

0.218

AC:

3341

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.363

AC:

1261

AN:

3470

East Asian (EAS)

AF:

0.0954

AC:

494

AN:

5180

South Asian (SAS)

AF:

0.242

AC:

1169

AN:

4824

European-Finnish (FIN)

AF:

0.414

AC:

4373

AN:

10556

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.368

AC:

25020

AN:

67968

Other (OTH)

AF:

0.270

AC:

570

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1520

3040

4559

6079

7599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

432

864

1296

1728

2160

<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:

0.326

Hom.:

16580

Bravo

AF:

0.249

Asia WGS

AF:

0.151

AC:

529

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.057

(source)

DANN

Benign

0.45

PhyloP100

-1.9

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over