rs2035254

Variant names:

• chr3-106090883-G-A
• rs2035254

Your query was ambiguous. Multiple possible variants found:

• chr3-106090883-G-A
• chr3-106090883-G-C
• chr3-106090883-G-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 0.611 in 152,004 control chromosomes in the GnomAD database, including 32,664 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 0.61 (32664 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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: 0.612 AC: 92938 AN: 151886 Hom.: 32667 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.611 AC: 92943 AN: 152004 Hom.: 32664 Cov.: 32 AF XY: 0.617 AC XY: 45866 AN XY: 74312

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.661

Alfa AF: 0.744 Hom.: 95399

Bravo AF: 0.590

Asia WGS AF: 0.763 AC: 2655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
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: rs2035254; hg19: chr3-105809730;