3-7810021-T-G

Variant names:

• chr3-7810021-T-G
• rs6443126

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.546 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

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.523

Alfa AF: 0.504 Hom.: 14026

Bravo AF: 0.546

Asia WGS AF: 0.444 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6443126; hg19: chr3-7851708;