chr3-7810021-T-G

Variant names:

• chr3-7810021-T-G
• rs6443126

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 0.546 in 151,722 control chromosomes in the GnomAD database, including 23,772 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 0.55 (23772 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 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: 0.546 AC: 82734 AN: 151604 Hom.: 23739 Cov.: 34

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.546 AC: 82819 AN: 151722 Hom.: 23772 Cov.: 34 AF XY: 0.538 AC XY: 39918 AN XY: 74136

African (AFR) AF: 0.721 AC: 29796 AN: 41330

American (AMR) AF: 0.414 AC: 6314 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1611 AN: 3470

East Asian (EAS) AF: 0.273 AC: 1407 AN: 5154

South Asian (SAS) AF: 0.516 AC: 2488 AN: 4818

European-Finnish (FIN) AF: 0.462 AC: 4874 AN: 10546

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.509 AC: 34535 AN: 67832

Other (OTH) AF: 0.523 AC: 1103 AN: 2108

Alfa AF: 0.517 Hom.: 48014

Bravo AF: 0.546

Asia WGS AF: 0.444 AC: 1545 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	0.39
DANN	Benign	0.50
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs6443126; hg19: chr3-7851708;