15-49794283-C-T

Variant names:

• chr15-49794283-C-T
• rs10519239
• ENST00000558657.1:n.38C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000558657.1(ENSG00000259388):​n.38C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0254 in 1,151,916 control chromosomes in the GnomAD database, including 536 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 0.036 (110 hom., cov: 32)
  • Exomes 𝑓: 0.024 (426 hom.)
• Consequence: ENSG00000259388 ENST00000558657.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.05
• Publications: 4 publications found

Genes affected

ENSG00000259388 (HGNC:):

RLIMP3 (HGNC:39684):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0358 (5455/152270) while in subpopulation AMR AF = 0.0422 (646/15296). AF 95% confidence interval is 0.0395. There are 110 homozygotes in GnomAd4. There are 2558 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 110 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RLIMP3		n.49794283C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259388	ENST00000558657.1	n.38C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0359 AC: 5455 AN: 152152 Hom.: 109 Cov.: 32

Gnomad AFR AF: 0.0369

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0423

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0406

Gnomad OTH AF: 0.0392

GnomAD4 exome AF: 0.0238 AC: 23748 AN: 999646 Hom.: 426 Cov.: 15 AF XY: 0.0240 AC XY: 12395 AN XY: 517028

African (AFR) AF: 0.0284 AC: 689 AN: 24240

American (AMR) AF: 0.0285 AC: 1171 AN: 41112

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 1310 AN: 22614

East Asian (EAS) AF: 0.0000797 AC: 3 AN: 37648

South Asian (SAS) AF: 0.0135 AC: 1011 AN: 75060

European-Finnish (FIN) AF: 0.0183 AC: 967 AN: 52986

Middle Eastern (MID) AF: 0.0242 AC: 116 AN: 4788

European-Non Finnish (NFE) AF: 0.0247 AC: 17215 AN: 696238

Other (OTH) AF: 0.0282 AC: 1266 AN: 44960

GnomAD4 genome AF: 0.0358 AC: 5455 AN: 152270 Hom.: 110 Cov.: 32 AF XY: 0.0343 AC XY: 2558 AN XY: 74470

African (AFR) AF: 0.0368 AC: 1530 AN: 41540

American (AMR) AF: 0.0422 AC: 646 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0110 AC: 53 AN: 4824

European-Finnish (FIN) AF: 0.0137 AC: 145 AN: 10606

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0406 AC: 2760 AN: 68028

Other (OTH) AF: 0.0388 AC: 82 AN: 2116

Alfa AF: 0.0377 Hom.: 159

Bravo AF: 0.0355

Asia WGS AF: 0.00722 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	3.7
DANN	Benign	0.78
PhyloP100		5.0

Splicing

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

Other links and lift over

dbSNP: rs10519239; hg19: chr15-50086480;