Genetic Variant ENSG00000283877:n.*195-7680C>T (chr3-46609503-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 ENST00000505797.1(ENSG00000283877):n.*195-7680C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0496 in 152,274 control chromosomes in the GnomAD database, including 242 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 0.050 ( 242 hom., cov: 32)

Consequence

ENSG00000283877
ENST00000505797.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.117

Publications

8 publications found

Variant links:

Genes affected

ENSG00000283877 (HGNC:):

ENSG00000283877 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=-0.75).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 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
ENSG00000283877	ENST00000505797.1 link	n.*195-7680C>T		intron_variant	Intron 3 of 3	3		ENSP00000490854.1		A0A1B0GWB0

Frequencies

GnomAD3 genomes

AF:

0.0497

AC:

7555

AN:

152156

Hom.:

242

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0227

Gnomad AMI

AF:

0.0901

Gnomad AMR

AF:

0.0688

Gnomad ASJ

AF:

0.0412

Gnomad EAS

AF:

0.147

Gnomad SAS

AF:

0.112

Gnomad FIN

AF:

0.0464

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0496

Gnomad OTH

AF:

0.0632

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0496

AC:

7559

AN:

152274

Hom.:

242

Cov.:

AF XY:

0.0516

AC XY:

3841

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.0228

AC:

949

AN:

41562

American (AMR)

AF:

0.0686

AC:

1050

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0412

AC:

143

AN:

3470

East Asian (EAS)

AF:

0.148

AC:

763

AN:

5168

South Asian (SAS)

AF:

0.112

AC:

538

AN:

4820

European-Finnish (FIN)

AF:

0.0464

AC:

492

AN:

10612

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0496

AC:

3376

AN:

68026

Other (OTH)

AF:

0.0620

AC:

131

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

364

728

1092

1456

1820

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

282

376

470

<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:

0.0345

Hom.:

Bravo

AF:

0.0502

Asia WGS

AF:

0.120

AC:

416

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

2.2

(source)

DANN

Benign

0.75

PhyloP100

0.12

Splicing

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

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over