2-226257500-G-T

Variant names:

• chr2-226257500-G-T
• rs1515110

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 0.642 in 151,898 control chromosomes in the GnomAD database, including 31,741 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 0.64 (31741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97363 AN: 151780 Hom.: 31709 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.642 AC: 97453 AN: 151898 Hom.: 31741 Cov.: 32 AF XY: 0.643 AC XY: 47729 AN XY: 74208

African (AFR) AF: 0.584 AC: 24169 AN: 41408

American (AMR) AF: 0.731 AC: 11160 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2473 AN: 3468

East Asian (EAS) AF: 0.921 AC: 4766 AN: 5172

South Asian (SAS) AF: 0.753 AC: 3632 AN: 4824

European-Finnish (FIN) AF: 0.610 AC: 6424 AN: 10530

Middle Eastern (MID) AF: 0.593 AC: 172 AN: 290

European-Non Finnish (NFE) AF: 0.630 AC: 42781 AN: 67920

Other (OTH) AF: 0.650 AC: 1374 AN: 2114

Alfa AF: 0.636 Hom.: 120263

Bravo AF: 0.648

Asia WGS AF: 0.829 AC: 2883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.60
DANN	Benign	0.21
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1515110; hg19: chr2-227122216;