rs1879316

Variant names:

• chr10-43273996-T-C
• rs1879316

Your query was ambiguous. Multiple possible variants found:

• chr10-43273996-T-C
• chr10-43273996-T-G

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 0.827 in 152,166 control chromosomes in the GnomAD database, including 52,535 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 0.83 (52535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 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: 0.827 AC: 125672 AN: 152048 Hom.: 52478 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.827 AC: 125793 AN: 152166 Hom.: 52535 Cov.: 32 AF XY: 0.823 AC XY: 61213 AN XY: 74400

African (AFR) AF: 0.806 AC: 33446 AN: 41472

American (AMR) AF: 0.762 AC: 11668 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2907 AN: 3470

East Asian (EAS) AF: 0.476 AC: 2453 AN: 5158

South Asian (SAS) AF: 0.758 AC: 3655 AN: 4822

European-Finnish (FIN) AF: 0.891 AC: 9450 AN: 10606

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59405 AN: 68012

Other (OTH) AF: 0.824 AC: 1741 AN: 2114

Alfa AF: 0.799 Hom.: 2457

Bravo AF: 0.818

Asia WGS AF: 0.631 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1879316; hg19: chr10-43769444;