rs2887180

Variant names:

• chr2-180584578-C-A
• rs2887180
• ENST00000429816.1:n.443-12747G>T

Variant summary

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

The ENST00000429816.1(ENSG00000225258):​n.443-12747G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,186 control chromosomes in the GnomAD database, including 4,376 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 (4376 hom., cov: 33)
• Consequence: ENSG00000225258 ENST00000429816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 2 publications found

Genes affected

ENSG00000225258 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225258	ENST00000429816.1	TSL:3	n.443-12747G>T		intron	N/A
	ENSG00000304108	ENST00000799803.1		n.160+19270C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34510 AN: 152070 Hom.: 4360 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.227 AC: 34561 AN: 152186 Hom.: 4376 Cov.: 33 AF XY: 0.233 AC XY: 17347 AN XY: 74414

African (AFR) AF: 0.196 AC: 8162 AN: 41538

American (AMR) AF: 0.344 AC: 5252 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3468

East Asian (EAS) AF: 0.490 AC: 2535 AN: 5170

South Asian (SAS) AF: 0.268 AC: 1292 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2288 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13747 AN: 68002

Other (OTH) AF: 0.211 AC: 446 AN: 2116

Alfa AF: 0.211 Hom.: 1842

Bravo AF: 0.235

Asia WGS AF: 0.393 AC: 1366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2887180; hg19: chr2-181449305;