2-35230275-A-T

Position:

• chr2-35230275-A-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 0.615 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.848

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.615

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726698; hg19: chr2-35455341;