chr2-175424591-G-A

Variant names:

• chr2-175424591-G-A
• rs2461751
• ENST00000438963.2:n.248-17857G>A

Variant summary

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

The ENST00000438963.2(ENSG00000229066):​n.248-17857G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,056 control chromosomes in the GnomAD database, including 4,512 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 0.23 (4512 hom., cov: 32)
• Consequence: ENSG00000229066 ENST00000438963.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 17 publications found

Genes affected

ENSG00000229066 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438963.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229066	ENST00000438963.2	TSL:3	n.248-17857G>A		intron	N/A
	ENSG00000229066	ENST00000444567.1	TSL:3	n.449-30017G>A		intron	N/A
	ENSG00000229066	ENST00000653625.1		n.337-17857G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34717 AN: 151938 Hom.: 4512 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.229 AC: 34749 AN: 152056 Hom.: 4512 Cov.: 32 AF XY: 0.231 AC XY: 17196 AN XY: 74308

African (AFR) AF: 0.305 AC: 12649 AN: 41478

American (AMR) AF: 0.264 AC: 4039 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3466

East Asian (EAS) AF: 0.547 AC: 2816 AN: 5150

South Asian (SAS) AF: 0.234 AC: 1125 AN: 4812

European-Finnish (FIN) AF: 0.149 AC: 1570 AN: 10572

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11021 AN: 67986

Other (OTH) AF: 0.243 AC: 514 AN: 2114

Alfa AF: 0.197 Hom.: 13490

Bravo AF: 0.242

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.77
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2461751; hg19: chr2-176289319;