chr6-32429626-T-G

Position:

• chr6-32429626-T-G

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 0.365 in 152,088 control chromosomes in the GnomAD database, including 10,593 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 0.37 (10593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.494 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: 0.366 AC: 55548 AN: 151970 Hom.: 10587 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.365 AC: 55570 AN: 152088 Hom.: 10593 Cov.: 32 AF XY: 0.367 AC XY: 27315 AN XY: 74348

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.390

Alfa AF: 0.397 Hom.: 16610

Bravo AF: 0.371

Asia WGS AF: 0.445 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9268585; hg19: chr6-32397403;