6-95559467-T-C

Variant names:

• chr6-95559467-T-C
• rs10782175

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 0.722 in 151,824 control chromosomes in the GnomAD database, including 40,157 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 0.72 (40157 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 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: 0.722 AC: 109538 AN: 151706 Hom.: 40113 Cov.: 30

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.722 AC: 109635 AN: 151824 Hom.: 40157 Cov.: 30 AF XY: 0.721 AC XY: 53543 AN XY: 74230

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.718

Alfa AF: 0.669 Hom.: 30177

Bravo AF: 0.720

Asia WGS AF: 0.796 AC: 2759 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10782175; hg19: chr6-96007343;