2-18503808-A-G

Variant names:

• chr2-18503808-A-G
• rs2345724
• ENST00000670548.1:n.2547A>G

Variant summary

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

The ENST00000670548.1(ENSG00000287881):​n.2547A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0324 in 152,224 control chromosomes in the GnomAD database, including 105 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 0.032 (105 hom., cov: 32)
• Consequence: ENSG00000287881 ENST00000670548.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 0 publications found

Genes affected

ENSG00000287881 (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 (SAS) allele frequency at 95% confidence interval = 0.0728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373454	XR_001739302.1	n.903+2262A>G		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287881	ENST00000670548.1	n.2547A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000287849	ENST00000668609.2	n.905-875T>C		intron_variant	Intron 2 of 4
ENSG00000287849	ENST00000690447.2	n.270+10375T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0324 AC: 4926 AN: 152106 Hom.: 104 Cov.: 32

Gnomad AFR AF: 0.00992

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0323

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.0169

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0427

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0324 AC: 4926 AN: 152224 Hom.: 105 Cov.: 32 AF XY: 0.0330 AC XY: 2453 AN XY: 74432

African (AFR) AF: 0.00989 AC: 411 AN: 41552

American (AMR) AF: 0.0323 AC: 493 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3468

East Asian (EAS) AF: 0.0555 AC: 287 AN: 5170

South Asian (SAS) AF: 0.0794 AC: 383 AN: 4824

European-Finnish (FIN) AF: 0.0169 AC: 179 AN: 10604

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0427 AC: 2906 AN: 68012

Other (OTH) AF: 0.0355 AC: 75 AN: 2112

Alfa AF: 0.0439 Hom.: 128

Bravo AF: 0.0318

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.86
DANN	Benign	0.69
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs2345724; hg19: chr2-18685074;