chr4-167510453-T-C

Variant names:

• chr4-167510453-T-C
• rs10517942

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 0.356 in 151,864 control chromosomes in the GnomAD database, including 9,918 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 0.36 (9918 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 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: 0.356 AC: 54084 AN: 151744 Hom.: 9919 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.356 AC: 54116 AN: 151864 Hom.: 9918 Cov.: 31 AF XY: 0.362 AC XY: 26833 AN XY: 74212

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.387

Alfa AF: 0.378 Hom.: 17170

Bravo AF: 0.355

Asia WGS AF: 0.438 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517942; hg19: chr4-168431604;