chr10-6360717-C-G

Position:

• chr10-6360717-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;