rs7761213

Variant names:

• chr6-24028175-T-C
• rs7761213

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.672 in 152,032 control chromosomes in the GnomAD database, including 34,482 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 0.67 (34482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.38
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.71 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

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102124 AN: 151914 Hom.: 34448 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.672 AC: 102217 AN: 152032 Hom.: 34482 Cov.: 32 AF XY: 0.672 AC XY: 49898 AN XY: 74282

African (AFR) AF: 0.654 AC: 27122 AN: 41468

American (AMR) AF: 0.721 AC: 11013 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2086 AN: 3466

East Asian (EAS) AF: 0.718 AC: 3701 AN: 5158

South Asian (SAS) AF: 0.620 AC: 2989 AN: 4818

European-Finnish (FIN) AF: 0.690 AC: 7287 AN: 10564

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45759 AN: 67968

Other (OTH) AF: 0.644 AC: 1359 AN: 2110

Alfa AF: 0.674 Hom.: 141495

Bravo AF: 0.675

Asia WGS AF: 0.672 AC: 2340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.56
PhyloP100		-5.4

Splicing

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

Other links and lift over

dbSNP: rs7761213; hg19: chr6-24028403;