2-226233671-A-G

Variant names:

• chr2-226233671-A-G
• rs1515114

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 0.461 in 152,020 control chromosomes in the GnomAD database, including 16,396 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 0.46 (16396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.531 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: 0.461 AC: 70033 AN: 151902 Hom.: 16374 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.461 AC: 70089 AN: 152020 Hom.: 16396 Cov.: 32 AF XY: 0.457 AC XY: 33966 AN XY: 74312

African (AFR) AF: 0.384 AC: 15935 AN: 41468

American (AMR) AF: 0.541 AC: 8259 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1989 AN: 3466

East Asian (EAS) AF: 0.480 AC: 2481 AN: 5170

South Asian (SAS) AF: 0.519 AC: 2501 AN: 4818

European-Finnish (FIN) AF: 0.398 AC: 4212 AN: 10572

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33173 AN: 67950

Other (OTH) AF: 0.494 AC: 1041 AN: 2108

Alfa AF: 0.484 Hom.: 57154

Bravo AF: 0.468

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	9.9
DANN	Benign	0.77
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs1515114; hg19: chr2-227098387;