6-32434687-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 0.387 in 152,012 control chromosomes in the GnomAD database, including 11,698 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 0.39 (11698 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58747 AN: 151894 Hom.: 11697 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.387 AC: 58768 AN: 152012 Hom.: 11698 Cov.: 31 AF XY: 0.389 AC XY: 28889 AN XY: 74300

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.413

Alfa AF: 0.389 Hom.: 6030

Bravo AF: 0.395

Asia WGS AF: 0.473 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.9
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7773756; hg19: chr6-32402464;