6-32698518-A-G

Position:

• chr6-32698518-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 0.146 in 152,136 control chromosomes in the GnomAD database, including 1,908 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 0.15 (1908 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 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: 0.146 AC: 22213 AN: 152018 Hom.: 1900 Cov.: 30

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.146 AC: 22251 AN: 152136 Hom.: 1908 Cov.: 30 AF XY: 0.152 AC XY: 11322 AN XY: 74376

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.0811

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.139

Alfa AF: 0.143 Hom.: 998

Bravo AF: 0.155

Asia WGS AF: 0.111 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.5
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275319; hg19: chr6-32666295;