10-113357067-C-T

Variant names:

• chr10-113357067-C-T
• rs10885436

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 0.51 in 152,054 control chromosomes in the GnomAD database, including 22,780 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 0.51 (22780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 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: 0.511 AC: 77622 AN: 151936 Hom.: 22792 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.510 AC: 77605 AN: 152054 Hom.: 22780 Cov.: 32 AF XY: 0.511 AC XY: 37965 AN XY: 74344

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.529

Alfa AF: 0.505 Hom.: 2672

Bravo AF: 0.488

Asia WGS AF: 0.255 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10885436; hg19: chr10-115116826;