rs3135461

Variant names:

• chr6-32712345-G-A
• rs3135461

Your query was ambiguous. Multiple possible variants found:

• chr6-32712345-G-A
• chr6-32712345-G-C

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 0.77 in 151,498 control chromosomes in the GnomAD database, including 45,107 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 0.77 (45107 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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: 0.770 AC: 116531 AN: 151380 Hom.: 45066 Cov.: 30

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.770 AC: 116629 AN: 151498 Hom.: 45107 Cov.: 30 AF XY: 0.770 AC XY: 57010 AN XY: 74052

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.796

Alfa AF: 0.769 Hom.: 18506

Bravo AF: 0.775

Asia WGS AF: 0.855 AC: 2976 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	2.8
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3135461; hg19: chr6-32680122;