6-32786304-T-C

Position:

• chr6-32786304-T-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 0.646 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.32786304T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;