10-6393195-G-C

Position:

• chr10-6393195-G-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 0.137 in 152,044 control chromosomes in the GnomAD database, including 1,525 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 0.14 (1525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.179 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: 0.137 AC: 20763 AN: 151924 Hom.: 1520 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.0933

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.137 AC: 20799 AN: 152044 Hom.: 1525 Cov.: 32 AF XY: 0.140 AC XY: 10404 AN XY: 74330

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0932

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.117

Alfa AF: 0.121 Hom.: 156

Bravo AF: 0.130

Asia WGS AF: 0.177 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12257237; hg19: chr10-6435157;