dbSNP rs10484676: ENSG00000287976:n.49-35216T>C (chr6-147983562-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 ENST00000773311.1(ENSG00000287976):n.49-35216T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.088 in 152,288 control chromosomes in the GnomAD database, including 607 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 0.088 ( 607 hom., cov: 33)

Consequence

ENSG00000287976
ENST00000773311.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.11

Publications

0 publications found

Variant links:

Genes affected

ENSG00000287976 (HGNC:):

ENSG00000287976 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 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
ENSG00000287976	ENST00000773311.1 link	n.49-35216T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0880

AC:

13392

AN:

152170

Hom.:

608

Cov.:

show subpopulations

Gnomad AFR

AF:

0.110

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.0570

Gnomad ASJ

AF:

0.0381

Gnomad EAS

AF:

0.0113

Gnomad SAS

AF:

0.0128

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0931

Gnomad OTH

AF:

0.0765

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

GnomAD4 genome

AF:

0.0880

AC:

13405

AN:

152288

Hom.:

607

Cov.:

AF XY:

0.0861

AC XY:

6414

AN XY:

74468

show subpopulations

African (AFR)

AF:

0.110

AC:

4572

AN:

41558

American (AMR)

AF:

0.0570

AC:

873

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0381

AC:

132

AN:

3468

East Asian (EAS)

AF:

0.0112

AC:

AN:

5190

South Asian (SAS)

AF:

0.0130

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.107

AC:

1130

AN:

10602

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0931

AC:

6329

AN:

68012

Other (OTH)

AF:

0.0757

AC:

160

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

608

1217

1825

2434

3042

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

150

300

450

600

750

<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:

0.0880

Hom.:

313

Bravo

AF:

0.0865

Asia WGS

AF:

0.0260

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.15

(source)

DANN

Benign

0.77

PhyloP100

-2.1

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over