chr10-113996371-T-C

Position:

• chr10-113996371-T-C

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 0.924 in 152,206 control chromosomes in the GnomAD database, including 65,310 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 0.92 (65310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140468 AN: 152088 Hom.: 65267 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.924 AC: 140569 AN: 152206 Hom.: 65310 Cov.: 32 AF XY: 0.926 AC XY: 68922 AN XY: 74424

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.950

Gnomad4 ASJ AF: 0.953

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.992

Gnomad4 FIN AF: 0.988

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.935

Alfa AF: 0.960 Hom.: 150874

Bravo AF: 0.914

Asia WGS AF: 0.982 AC: 3415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs82625; hg19: chr10-115756130;