rs3135005

Variant names:

• chr6-32618242-A-G
• rs3135005

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 0.862 in 152,056 control chromosomes in the GnomAD database, including 56,645 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 0.86 (56645 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.899 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: 0.862 AC: 131041 AN: 151938 Hom.: 56600 Cov.: 30

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.862 AC: 131143 AN: 152056 Hom.: 56645 Cov.: 30 AF XY: 0.861 AC XY: 64027 AN XY: 74330

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.912

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.891

Alfa AF: 0.855 Hom.: 35594

Bravo AF: 0.869

Asia WGS AF: 0.790 AC: 2751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3135005; hg19: chr6-32586019;