rs7764819

Variant names:

• chr6-32712799-T-G
• rs7764819

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 0.104 in 152,276 control chromosomes in the GnomAD database, including 900 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 0.10 (900 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15811 AN: 152158 Hom.: 900 Cov.: 33

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0724

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0828

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

GnomAD4 genome AF: 0.104 AC: 15829 AN: 152276 Hom.: 900 Cov.: 33 AF XY: 0.106 AC XY: 7898 AN XY: 74454

African (AFR) AF: 0.0904 AC: 3757 AN: 41548

American (AMR) AF: 0.117 AC: 1787 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0724 AC: 251 AN: 3468

East Asian (EAS) AF: 0.104 AC: 539 AN: 5180

South Asian (SAS) AF: 0.0251 AC: 121 AN: 4828

European-Finnish (FIN) AF: 0.181 AC: 1921 AN: 10606

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7219 AN: 68026

Other (OTH) AF: 0.0824 AC: 174 AN: 2112

Alfa AF: 0.107 Hom.: 1576

Bravo AF: 0.102

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.89
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs7764819; hg19: chr6-32680576;