rs6773514

Variant names:

• chr3-138844803-C-A
• rs6773514

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 0.378 in 150,876 control chromosomes in the GnomAD database, including 11,619 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 0.38 (11619 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.378 AC: 56959 AN: 150760 Hom.: 11621 Cov.: 29

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.0134

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.378 AC: 56970 AN: 150876 Hom.: 11619 Cov.: 29 AF XY: 0.366 AC XY: 26979 AN XY: 73642

African (AFR) AF: 0.305 AC: 12500 AN: 41040

American (AMR) AF: 0.321 AC: 4844 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1800 AN: 3472

East Asian (EAS) AF: 0.0132 AC: 67 AN: 5060

South Asian (SAS) AF: 0.340 AC: 1620 AN: 4764

European-Finnish (FIN) AF: 0.332 AC: 3449 AN: 10404

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.461 AC: 31261 AN: 67786

Other (OTH) AF: 0.404 AC: 844 AN: 2088

Alfa AF: 0.412 Hom.: 2316

Bravo AF: 0.369

Asia WGS AF: 0.176 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs6773514; hg19: chr3-138563645;