rs231390

Variant names:

• chr2-203770044-G-A
• rs231390

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 0.618 in 152,144 control chromosomes in the GnomAD database, including 29,484 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 0.62 (29484 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.652 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: 0.618 AC: 93959 AN: 152026 Hom.: 29475 Cov.: 33

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.618 AC: 94006 AN: 152144 Hom.: 29484 Cov.: 33 AF XY: 0.618 AC XY: 45984 AN XY: 74370

African (AFR) AF: 0.561 AC: 23279 AN: 41506

American (AMR) AF: 0.625 AC: 9549 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1936 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1857 AN: 5168

South Asian (SAS) AF: 0.668 AC: 3222 AN: 4824

European-Finnish (FIN) AF: 0.705 AC: 7457 AN: 10574

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44677 AN: 68000

Other (OTH) AF: 0.582 AC: 1230 AN: 2112

Alfa AF: 0.628 Hom.: 46907

Bravo AF: 0.607

Asia WGS AF: 0.512 AC: 1779 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	6.0
DANN	Benign	0.61
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs231390; hg19: chr2-204634767;