chr6-32786304-T-C

Variant names:

• chr6-32786304-T-C
• rs2261566

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 0.646 in 151,908 control chromosomes in the GnomAD database, including 31,817 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 0.65 (31817 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

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 = 0.716 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: 0.646 AC: 98095 AN: 151790 Hom.: 31796 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.646 AC: 98160 AN: 151908 Hom.: 31817 Cov.: 31 AF XY: 0.650 AC XY: 48285 AN XY: 74246

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.634

Alfa AF: 0.637 Hom.: 8588

Bravo AF: 0.640

Asia WGS AF: 0.740 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2261566; hg19: chr6-32754081;