rs3135338

chr6-32433440-C-T

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 0.626 in 152,040 control chromosomes in the GnomAD database, including 30,303 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 0.63 (30303 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 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: 0.626 AC: 95063 AN: 151922 Hom.: 30300 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.626 AC: 95107 AN: 152040 Hom.: 30303 Cov.: 33 AF XY: 0.631 AC XY: 46855 AN XY: 74312

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.647

Alfa AF: 0.670 Hom.: 48266

Bravo AF: 0.615

Asia WGS AF: 0.675 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.27
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3135338; hg19: chr6-32401217;