chr10-47316507-T-C

Position:

• chr10-47316507-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 0.921 in 152,138 control chromosomes in the GnomAD database, including 64,637 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 (64637 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.921 AC: 139978 AN: 152020 Hom.: 64586 Cov.: 30

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.921 AC: 140091 AN: 152138 Hom.: 64637 Cov.: 30 AF XY: 0.919 AC XY: 68318 AN XY: 74350

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.963

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.922

Alfa AF: 0.932 Hom.: 45879

Bravo AF: 0.917

Asia WGS AF: 0.788 AC: 2742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.6
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9421801; hg19: chr10-48422855;