6-32457105-T-C

Variant names:

• chr6-32457105-T-C
• rs7763262

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 0.705 in 152,070 control chromosomes in the GnomAD database, including 38,043 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 0.70 (38043 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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 (SAS) allele frequency at 95% confidence interval = 0.786 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: 0.705 AC: 107110 AN: 151952 Hom.: 38005 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.705 AC: 107203 AN: 152070 Hom.: 38043 Cov.: 31 AF XY: 0.708 AC XY: 52609 AN XY: 74334

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.737

Alfa AF: 0.687 Hom.: 48215

Bravo AF: 0.715

Asia WGS AF: 0.739 AC: 2574 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	6.6
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7763262; hg19: chr6-32424882;