rs2248359

Variant names:

• chr20-54174979-C-T
• rs2248359
• ENST00000792347.1:n.351C>T

Variant summary

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

The ENST00000792347.1(ENSG00000286587):​n.351C>T 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 0.464 in 152,020 control chromosomes in the GnomAD database, including 17,317 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 0.46 (17317 hom., cov: 32)
• Consequence: ENSG00000286587 ENST00000792347.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 142 publications found

Genes affected

ENSG00000286587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286587	ENST00000792347.1	n.351C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000286587	ENST00000655028.2	n.569+50C>T		intron_variant	Intron 3 of 4
ENSG00000286587	ENST00000792273.1	n.288+6408C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70423 AN: 151902 Hom.: 17272 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.464 AC: 70521 AN: 152020 Hom.: 17317 Cov.: 32 AF XY: 0.460 AC XY: 34209 AN XY: 74294

African (AFR) AF: 0.643 AC: 26682 AN: 41468

American (AMR) AF: 0.371 AC: 5675 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1973 AN: 3472

East Asian (EAS) AF: 0.372 AC: 1924 AN: 5174

South Asian (SAS) AF: 0.413 AC: 1989 AN: 4814

European-Finnish (FIN) AF: 0.355 AC: 3753 AN: 10562

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 27001 AN: 67948

Other (OTH) AF: 0.479 AC: 1008 AN: 2104

Alfa AF: 0.420 Hom.: 64270

Bravo AF: 0.471

Asia WGS AF: 0.417 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.76
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2248359; hg19: chr20-52791518; COSMIC: COSV53775496;