rs3135005

Positions:

• chr6-32618242-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 0.862 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;