2-232508056-C-G

Variant names:

• chr2-232508056-C-G
• rs1881494
• ENST00000782985.1:n.209+5190C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000782985.1(ENSG00000301941):​n.209+5190C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000301941 ENST00000782985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 2 publications found

Genes affected

ENSG00000301941 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782985.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301941	ENST00000782985.1		n.209+5190C>G		intron	N/A
	ENSG00000301941	ENST00000782986.1		n.157+536C>G		intron	N/A

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

African (AFR) AF: 0.664 AC: 27515 AN: 41460

American (AMR) AF: 0.814 AC: 12452 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2829 AN: 3470

East Asian (EAS) AF: 0.956 AC: 4942 AN: 5172

South Asian (SAS) AF: 0.834 AC: 4017 AN: 4818

European-Finnish (FIN) AF: 0.819 AC: 8674 AN: 10590

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52910 AN: 68008

Other (OTH) AF: 0.756 AC: 1596 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.43
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1881494; hg19: chr2-233372766;