rs3135352

Variant names:

• chr6-32425129-C-A
• rs3135352

Your query was ambiguous. Multiple possible variants found:

• chr6-32425129-C-A
• chr6-32425129-C-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 0.906 in 152,238 control chromosomes in the GnomAD database, including 62,646 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 0.91 (62646 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.906 AC: 137803 AN: 152120 Hom.: 62593 Cov.: 31

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.927

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.980

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.931

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

GnomAD4 genome AF: 0.906 AC: 137914 AN: 152238 Hom.: 62646 Cov.: 31 AF XY: 0.907 AC XY: 67548 AN XY: 74442

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.980

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.933

Alfa AF: 0.878 Hom.: 31799

Bravo AF: 0.913

Asia WGS AF: 0.981 AC: 3413 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	0.050
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3135352; hg19: chr6-32392906;