6-32432311-C-T

Variant names:

• chr6-32432311-C-T
• rs984778

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;