rs6940110

chr6-10268831-T-Cchr6-10268831-T-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 0.441 in 152,098 control chromosomes in the GnomAD database, including 15,151 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 0.44 (15151 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.822

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.539 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: 0.441 AC: 67023 AN: 151980 Hom.: 15136 Cov.: 33

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.441 AC: 67077 AN: 152098 Hom.: 15151 Cov.: 33 AF XY: 0.436 AC XY: 32426 AN XY: 74344

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.485

Alfa AF: 0.461 Hom.: 33155

Bravo AF: 0.457

Asia WGS AF: 0.348 AC: 1210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	12
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6940110; hg19: chr6-10269064;