3-6375092-T-C

Variant names:

• chr3-6375092-T-C
• rs10510333

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 0.767 in 152,118 control chromosomes in the GnomAD database, including 44,944 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 0.77 (44944 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 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: 0.767 AC: 116606 AN: 151998 Hom.: 44898 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.767 AC: 116711 AN: 152118 Hom.: 44944 Cov.: 32 AF XY: 0.765 AC XY: 56880 AN XY: 74360

African (AFR) AF: 0.795 AC: 32967 AN: 41480

American (AMR) AF: 0.790 AC: 12058 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2311 AN: 3470

East Asian (EAS) AF: 0.803 AC: 4145 AN: 5164

South Asian (SAS) AF: 0.624 AC: 3013 AN: 4826

European-Finnish (FIN) AF: 0.780 AC: 8272 AN: 10602

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51607 AN: 67994

Other (OTH) AF: 0.724 AC: 1528 AN: 2110

Alfa AF: 0.761 Hom.: 81574

Bravo AF: 0.772

Asia WGS AF: 0.732 AC: 2543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.15
DANN	Benign	0.64
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs10510333; hg19: chr3-6416779;