6-32598621-G-A

Position:

• chr6-32598621-G-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 0.126 in 152,162 control chromosomes in the GnomAD database, including 1,527 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 (1527 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 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: 0.126 AC: 19219 AN: 152044 Hom.: 1526 Cov.: 33

Gnomad AFR AF: 0.0482

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0711

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.126 AC: 19237 AN: 152162 Hom.: 1527 Cov.: 33 AF XY: 0.125 AC XY: 9316 AN XY: 74382

Gnomad4 AFR AF: 0.0483

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0714

Gnomad4 SAS AF: 0.0723

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.114

Alfa AF: 0.147 Hom.: 350

Bravo AF: 0.133

Asia WGS AF: 0.0730 AC: 255 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.2
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: rs2760985; hg19: chr6-32566398;