2-232508056-C-G

Position:

• chr2-232508056-C-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;