chr6-32716610-A-G

Position:

• chr6-32716610-A-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 0.131 in 152,110 control chromosomes in the GnomAD database, including 1,379 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 (1379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19912 AN: 151992 Hom.: 1373 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.131 AC: 19950 AN: 152110 Hom.: 1379 Cov.: 32 AF XY: 0.131 AC XY: 9761 AN XY: 74352

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.0763

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.108

Alfa AF: 0.125 Hom.: 401

Bravo AF: 0.134

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	15
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275618; hg19: chr6-32684387;