rs3755015

Variant names:

• chr2-85536918-G-A
• rs3755015

Your query was ambiguous. Multiple possible variants found:

• chr2-85536918-G-A
• chr2-85536918-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 0.531 in 152,124 control chromosomes in the GnomAD database, including 22,841 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 0.53 (22841 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 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: 0.530 AC: 80638 AN: 152006 Hom.: 22806 Cov.: 33

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.531 AC: 80728 AN: 152124 Hom.: 22841 Cov.: 33 AF XY: 0.527 AC XY: 39160 AN XY: 74356

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.522

Alfa AF: 0.474 Hom.: 8647

Bravo AF: 0.536

Asia WGS AF: 0.441 AC: 1535 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3755015; hg19: chr2-85764041;