rs231390

Positions:

• chr2-203770044-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;