rs231390

Variant names:

• chr2-203770044-G-A
• rs231390

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.705

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.582

Alfa AF: 0.634 Hom.: 30585

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs231390; hg19: chr2-204634767;