rs4589502

Positions:

• chr15-66862731-C-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000617013.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105376718	XR_932381.3	n.15803-1138C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000617013.1	n.2429C>T		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.133

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.0845

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.173

Alfa AF: 0.172 Hom.: 499

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4589502; hg19: chr15-67155069;