rs4589502

Variant names:

• chr15-66862731-C-T
• rs4589502
• ENST00000617013.1:n.2429C>T

Variant summary

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

The ENST00000617013.1(ENSG00000277152):​n.2429C>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 0.189 in 152,178 control chromosomes in the GnomAD database, including 3,766 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 0.19 (3765 hom., cov: 32)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: ENSG00000277152 ENST00000617013.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 11 publications found

Genes affected

ENSG00000277152 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376718	XR_932381.3	n.15803-1138C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000277152	ENST00000617013.1	n.2429C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28657 AN: 152014 Hom.: 3753 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0789

Gnomad FIN AF: 0.0845

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.172

GnomAD4 exome AF: 0.130 AC: 6 AN: 46 Hom.: 1 Cov.: 0 AF XY: 0.132 AC XY: 5 AN XY: 38

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.133 AC: 4 AN: 30

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.189 AC: 28707 AN: 152132 Hom.: 3765 Cov.: 32 AF XY: 0.188 AC XY: 13949 AN XY: 74384

African (AFR) AF: 0.363 AC: 15033 AN: 41460

American (AMR) AF: 0.256 AC: 3919 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3470

East Asian (EAS) AF: 0.146 AC: 757 AN: 5180

South Asian (SAS) AF: 0.0788 AC: 380 AN: 4822

European-Finnish (FIN) AF: 0.0845 AC: 896 AN: 10602

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6839 AN: 67994

Other (OTH) AF: 0.173 AC: 365 AN: 2112

Alfa AF: 0.178 Hom.: 545

Bravo AF: 0.213

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.35
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4589502; hg19: chr15-67155069;