chr10-111074874-T-C

Variant names:

• chr10-111074874-T-C
• rs491589

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 0.835 in 152,170 control chromosomes in the GnomAD database, including 53,163 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 (53163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.869 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: 0.835 AC: 126946 AN: 152052 Hom.: 53142 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.835 AC: 127013 AN: 152170 Hom.: 53163 Cov.: 32 AF XY: 0.835 AC XY: 62083 AN XY: 74380

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.868

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.811

Alfa AF: 0.841 Hom.: 28139

Bravo AF: 0.832

Asia WGS AF: 0.779 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs491589; hg19: chr10-112834632;