chr3-102029794-A-G

Variant names:

• chr3-102029794-A-G
• rs771767

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 0.705 in 151,938 control chromosomes in the GnomAD database, including 38,215 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 0.70 (38215 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.705 AC: 107025 AN: 151822 Hom.: 38201 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.705 AC: 107078 AN: 151938 Hom.: 38215 Cov.: 32 AF XY: 0.709 AC XY: 52674 AN XY: 74306

African (AFR) AF: 0.605 AC: 25060 AN: 41424

American (AMR) AF: 0.719 AC: 10959 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2565 AN: 3466

East Asian (EAS) AF: 0.987 AC: 5124 AN: 5192

South Asian (SAS) AF: 0.706 AC: 3390 AN: 4802

European-Finnish (FIN) AF: 0.810 AC: 8592 AN: 10608

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49033 AN: 67906

Other (OTH) AF: 0.697 AC: 1466 AN: 2104

Alfa AF: 0.714 Hom.: 154633

Bravo AF: 0.695

Asia WGS AF: 0.831 AC: 2889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.38
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs771767; hg19: chr3-101748638;