2-180575354-G-A

Variant names:

• chr2-180575354-G-A
• rs1358520
• ENST00000429816.1:n.443-3523C>T

Variant summary

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

The ENST00000429816.1(ENSG00000225258):​n.443-3523C>T 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 151,300 control chromosomes in the GnomAD database, including 4,385 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 (4385 hom., cov: 32)
• Consequence: ENSG00000225258 ENST00000429816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225258	ENST00000429816.1	TSL:3	n.443-3523C>T		intron	N/A
	ENSG00000304108	ENST00000799803.1		n.160+10046G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34536 AN: 151182 Hom.: 4368 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.229 AC: 34592 AN: 151300 Hom.: 4385 Cov.: 32 AF XY: 0.234 AC XY: 17301 AN XY: 73918

African (AFR) AF: 0.198 AC: 8195 AN: 41358

American (AMR) AF: 0.345 AC: 5227 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3456

East Asian (EAS) AF: 0.493 AC: 2536 AN: 5140

South Asian (SAS) AF: 0.266 AC: 1279 AN: 4814

European-Finnish (FIN) AF: 0.211 AC: 2222 AN: 10506

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.205 AC: 13859 AN: 67572

Other (OTH) AF: 0.213 AC: 447 AN: 2096

Alfa AF: 0.221 Hom.: 10027

Bravo AF: 0.237

Asia WGS AF: 0.395 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.81
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs1358520; hg19: chr2-181440081;