10-35950228-C-T

Variant names:

• chr10-35950228-C-T
• rs913167

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 0.527 in 152,004 control chromosomes in the GnomAD database, including 21,238 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 0.53 (21238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 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: 0.527 AC: 80022 AN: 151884 Hom.: 21233 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.527 AC: 80057 AN: 152004 Hom.: 21238 Cov.: 32 AF XY: 0.522 AC XY: 38778 AN XY: 74294

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.560

Alfa AF: 0.556 Hom.: 5749

Bravo AF: 0.525

Asia WGS AF: 0.413 AC: 1441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs913167; hg19: chr10-36239156;