rs918959

Variant names:

• chr2-180649002-G-A
• rs918959
• ENST00000429816.1:n.225+43228C>T

Variant summary

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

The ENST00000429816.1(ENSG00000225258):​n.225+43228C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 152,058 control chromosomes in the GnomAD database, including 839 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 0.090 (839 hom., cov: 32)
• Consequence: ENSG00000225258 ENST00000429816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 13 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 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.225+43228C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0901 AC: 13691 AN: 151940 Hom.: 836 Cov.: 32

Gnomad AFR AF: 0.0414

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0854

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0901 AC: 13697 AN: 152058 Hom.: 839 Cov.: 32 AF XY: 0.0939 AC XY: 6976 AN XY: 74312

African (AFR) AF: 0.0414 AC: 1716 AN: 41486

American (AMR) AF: 0.192 AC: 2937 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1044 AN: 5154

South Asian (SAS) AF: 0.0727 AC: 350 AN: 4814

European-Finnish (FIN) AF: 0.110 AC: 1158 AN: 10566

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0854 AC: 5803 AN: 67982

Other (OTH) AF: 0.0856 AC: 181 AN: 2114

Alfa AF: 0.0892 Hom.: 2248

Bravo AF: 0.0957

Asia WGS AF: 0.116 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.7
DANN	Benign	0.74
PhyloP100		-0.29

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs918959;

hg19: chr2-181513729;