6-32432311-C-T

Position:

• chr6-32432311-C-T

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 0.625 in 151,726 control chromosomes in the GnomAD database, including 30,195 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 0.63 (30195 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94829 AN: 151608 Hom.: 30192 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.625 AC: 94873 AN: 151726 Hom.: 30195 Cov.: 31 AF XY: 0.630 AC XY: 46724 AN XY: 74136

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.648

Alfa AF: 0.661 Hom.: 21643

Bravo AF: 0.615

Asia WGS AF: 0.673 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs984778; hg19: chr6-32400088;