2-232515231-G-A

Variant names:

• chr2-232515231-G-A
• rs1656404

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 0.175 in 151,968 control chromosomes in the GnomAD database, including 2,466 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 0.18 (2466 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 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: 0.175 AC: 26590 AN: 151848 Hom.: 2464 Cov.: 31

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0249

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.175 AC: 26595 AN: 151968 Hom.: 2466 Cov.: 31 AF XY: 0.172 AC XY: 12750 AN XY: 74280

African (AFR) AF: 0.198 AC: 8195 AN: 41416

American (AMR) AF: 0.149 AC: 2271 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3468

East Asian (EAS) AF: 0.0251 AC: 130 AN: 5172

South Asian (SAS) AF: 0.143 AC: 689 AN: 4812

European-Finnish (FIN) AF: 0.148 AC: 1565 AN: 10574

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.186 AC: 12646 AN: 67942

Other (OTH) AF: 0.184 AC: 387 AN: 2104

Alfa AF: 0.177 Hom.: 4467

Bravo AF: 0.175

Asia WGS AF: 0.103 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.61
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1656404; hg19: chr2-233379941;