2-35230275-A-T

Variant names:

• chr2-35230275-A-T
• rs726698

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.615 in 151,422 control chromosomes in the GnomAD database, including 29,317 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 (29317 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.948 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93017 AN: 151306 Hom.: 29287 Cov.: 31

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.615 AC: 93100 AN: 151422 Hom.: 29317 Cov.: 31 AF XY: 0.626 AC XY: 46269 AN XY: 73948

African (AFR) AF: 0.615 AC: 25446 AN: 41348

American (AMR) AF: 0.685 AC: 10393 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1738 AN: 3464

East Asian (EAS) AF: 0.970 AC: 4964 AN: 5116

South Asian (SAS) AF: 0.848 AC: 4082 AN: 4812

European-Finnish (FIN) AF: 0.622 AC: 6531 AN: 10508

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38011 AN: 67690

Other (OTH) AF: 0.615 AC: 1301 AN: 2114

Alfa AF: 0.583 Hom.: 3221

Bravo AF: 0.615

Asia WGS AF: 0.860 AC: 2967 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.55
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs726698; hg19: chr2-35455341;