rs1548587

Variant names:

• chr5-138457050-A-G
• rs1548587
• ENST00000728999.1:n.88A>G

Variant summary

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

The ENST00000728999.1(ENSG00000295283):​n.88A>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 0.528 in 151,736 control chromosomes in the GnomAD database, including 21,990 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 0.53 (21990 hom., cov: 31)
• Consequence: ENSG00000295283 ENST00000728999.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 3 publications found

Genes affected

ENSG00000295283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.573 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
ENSG00000295283	ENST00000728999.1	n.88A>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000295261	ENST00000728909.1	n.85+1394T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79980 AN: 151626 Hom.: 21954 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.528 AC: 80071 AN: 151736 Hom.: 21990 Cov.: 31 AF XY: 0.526 AC XY: 39002 AN XY: 74138

African (AFR) AF: 0.454 AC: 18772 AN: 41330

American (AMR) AF: 0.571 AC: 8709 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2067 AN: 3470

East Asian (EAS) AF: 0.179 AC: 928 AN: 5170

South Asian (SAS) AF: 0.367 AC: 1760 AN: 4792

European-Finnish (FIN) AF: 0.655 AC: 6877 AN: 10500

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39263 AN: 67906

Other (OTH) AF: 0.539 AC: 1137 AN: 2110

Alfa AF: 0.545 Hom.: 6045

Bravo AF: 0.518

Asia WGS AF: 0.305 AC: 1060 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.26
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1548587; hg19: chr5-137792739;