2-232508056-C-G

Variant names:

• chr2-232508056-C-G
• rs1881494

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 0.762 in 152,126 control chromosomes in the GnomAD database, including 44,473 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 0.76 (44473 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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: 0.762 AC: 115759 AN: 152008 Hom.: 44424 Cov.: 33

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.762 AC: 115861 AN: 152126 Hom.: 44473 Cov.: 33 AF XY: 0.766 AC XY: 56992 AN XY: 74372

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.814

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.756

Alfa AF: 0.714 Hom.: 2198

Bravo AF: 0.759

Asia WGS AF: 0.854 AC: 2966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1881494; hg19: chr2-233372766;