chr2-18503808-A-G

Position:

• chr2-18503808-A-G

Variant summary

Our verdict is Benign. Variant got -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: ENST00000670548.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105373454	XR_001739302.1	n.903+2262A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670548.1	n.2547A>G		non_coding_transcript_exon_variant	3/3
	ENST00000690447.1	n.270+10375T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00989

Gnomad4 AMR AF: 0.0323

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.0555

Gnomad4 SAS AF: 0.0794

Gnomad4 FIN AF: 0.0169

Gnomad4 NFE AF: 0.0427

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0448 Hom.: 101

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2345724; hg19: chr2-18685074;