chr2-203875952-G-A

Variant names:

• chr2-203875952-G-A
• rs231725

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 0.378 in 151,998 control chromosomes in the GnomAD database, including 11,298 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 0.38 (11298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 38 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 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: 0.378 AC: 57396 AN: 151880 Hom.: 11286 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.378 AC: 57453 AN: 151998 Hom.: 11298 Cov.: 32 AF XY: 0.385 AC XY: 28574 AN XY: 74276

African (AFR) AF: 0.417 AC: 17288 AN: 41436

American (AMR) AF: 0.393 AC: 6007 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3468

East Asian (EAS) AF: 0.591 AC: 3062 AN: 5184

South Asian (SAS) AF: 0.280 AC: 1346 AN: 4812

European-Finnish (FIN) AF: 0.485 AC: 5111 AN: 10534

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22601 AN: 67950

Other (OTH) AF: 0.329 AC: 694 AN: 2112

Alfa AF: 0.372 Hom.: 1508

Bravo AF: 0.376

Asia WGS AF: 0.392 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.27
DANN	Benign	0.82
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs231725; hg19: chr2-204740675;