rs6764623

Variant names:

• chr3-1004354-A-C
• rs6764623

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 0.296 in 151,868 control chromosomes in the GnomAD database, including 7,224 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 0.30 (7224 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 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: 0.296 AC: 44862 AN: 151748 Hom.: 7212 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.296 AC: 44912 AN: 151868 Hom.: 7224 Cov.: 32 AF XY: 0.295 AC XY: 21895 AN XY: 74208

African (AFR) AF: 0.392 AC: 16171 AN: 41288

American (AMR) AF: 0.246 AC: 3753 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1011 AN: 3470

East Asian (EAS) AF: 0.466 AC: 2398 AN: 5150

South Asian (SAS) AF: 0.313 AC: 1507 AN: 4816

European-Finnish (FIN) AF: 0.242 AC: 2565 AN: 10582

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.243 AC: 16553 AN: 67982

Other (OTH) AF: 0.298 AC: 630 AN: 2112

Alfa AF: 0.279 Hom.: 6804

Bravo AF: 0.299

Asia WGS AF: 0.422 AC: 1468 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6764623; hg19: chr3-1046038;