rs231723

Variant names:

• chr2-203875058-A-G
• rs231723

Your query was ambiguous. Multiple possible variants found:

• chr2-203875058-A-G
• chr2-203875058-A-T

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 0.398 in 152,016 control chromosomes in the GnomAD database, including 12,523 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 0.40 (12523 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 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: 0.398 AC: 60504 AN: 151898 Hom.: 12511 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.398 AC: 60557 AN: 152016 Hom.: 12523 Cov.: 32 AF XY: 0.405 AC XY: 30100 AN XY: 74292

African (AFR) AF: 0.371 AC: 15394 AN: 41478

American (AMR) AF: 0.411 AC: 6275 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3470

East Asian (EAS) AF: 0.647 AC: 3337 AN: 5160

South Asian (SAS) AF: 0.322 AC: 1548 AN: 4814

European-Finnish (FIN) AF: 0.529 AC: 5579 AN: 10548

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26166 AN: 67964

Other (OTH) AF: 0.355 AC: 750 AN: 2110

Alfa AF: 0.323 Hom.: 2139

Bravo AF: 0.392

Asia WGS AF: 0.445 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.7
DANN	Benign	0.76
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs231723; hg19: chr2-204739781;