rs1879316

Positions:

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

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 0.827 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.824

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1879316; hg19: chr10-43769444;