10-6360717-C-G

Variant names:

• chr10-6360717-C-G
• rs10752291

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 0.816 in 152,120 control chromosomes in the GnomAD database, including 50,700 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 0.82 (50700 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 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: 0.816 AC: 123976 AN: 152000 Hom.: 50657 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.816 AC: 124075 AN: 152120 Hom.: 50700 Cov.: 32 AF XY: 0.819 AC XY: 60883 AN XY: 74352

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.875

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.817

Alfa AF: 0.775 Hom.: 2678

Bravo AF: 0.817

Asia WGS AF: 0.908 AC: 3159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10752291; hg19: chr10-6402679;