chr6-32425168-C-A

Position:

• chr6-32425168-C-A

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 0.13 in 152,200 control chromosomes in the GnomAD database, including 1,537 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 0.13 (1537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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: 0.130 AC: 19748 AN: 152082 Hom.: 1537 Cov.: 32

Gnomad AFR AF: 0.0649

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0794

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.130 AC: 19755 AN: 152200 Hom.: 1537 Cov.: 32 AF XY: 0.128 AC XY: 9525 AN XY: 74388

Gnomad4 AFR AF: 0.0651

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0904

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.125

Alfa AF: 0.155 Hom.: 1586

Bravo AF: 0.120

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3135351; hg19: chr6-32392945;