6-32251066-A-G

Variant names:

• chr6-32251066-A-G
• rs3115573

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 0.415 in 152,032 control chromosomes in the GnomAD database, including 13,632 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 0.42 (13632 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63067 AN: 151914 Hom.: 13622 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.415 AC: 63100 AN: 152032 Hom.: 13632 Cov.: 32 AF XY: 0.414 AC XY: 30744 AN XY: 74322

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.447

Alfa AF: 0.453 Hom.: 16044

Bravo AF: 0.428

Asia WGS AF: 0.471 AC: 1640 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	1.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3115573; hg19: chr6-32218843;