ENST00000506902.2:n.669-14174C>T

Variant names:

• chr5-61217739-C-T
• rs34634
• ENST00000506902.2:n.669-14174C>T

Variant summary

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

The ENST00000506902.2(SMIM15-AS1):​n.669-14174C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,930 control chromosomes in the GnomAD database, including 17,040 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 0.47 (17040 hom., cov: 32)
• Consequence: SMIM15-AS1 ENST00000506902.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69
• Publications: 3 publications found

Genes affected

SMIM15-AS1 (HGNC:41293): (SMIM15 antisense RNA 1)

LINC02057 (HGNC:52900): (long intergenic non-protein coding RNA 2057)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM15-AS1	NR_109908.1	n.423-14174C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM15-AS1	ENST00000506902.2	n.669-14174C>T		intron_variant	Intron 3 of 3	3
LINC02057	ENST00000511794.6	n.470-16035G>A		intron_variant	Intron 2 of 2	3
LINC02057	ENST00000661728.1	n.551-16035G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70888 AN: 151812 Hom.: 17033 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.467 AC: 70905 AN: 151930 Hom.: 17040 Cov.: 32 AF XY: 0.468 AC XY: 34756 AN XY: 74264

African (AFR) AF: 0.415 AC: 17199 AN: 41412

American (AMR) AF: 0.456 AC: 6959 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1790 AN: 3468

East Asian (EAS) AF: 0.784 AC: 4057 AN: 5174

South Asian (SAS) AF: 0.428 AC: 2058 AN: 4810

European-Finnish (FIN) AF: 0.496 AC: 5236 AN: 10550

Middle Eastern (MID) AF: 0.507 AC: 147 AN: 290

European-Non Finnish (NFE) AF: 0.469 AC: 31889 AN: 67940

Other (OTH) AF: 0.486 AC: 1025 AN: 2108

Alfa AF: 0.476 Hom.: 7255

Bravo AF: 0.467

Asia WGS AF: 0.604 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.3
DANN	Benign	0.72
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs34634; hg19: chr5-60513566;