ENST00000524295.5:n.94-137C>T

Variant names:

• chr5-151950837-C-T
• rs4958287
• ENST00000524295.5:n.94-137C>T

Variant summary

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

The ENST00000524295.5(LINC01933):​n.94-137C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,208 control chromosomes in the GnomAD database, including 3,811 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 0.21 (3810 hom., cov: 33)
  • Exomes 𝑓: 0.32 (1 hom.)
• Consequence: LINC01933 ENST00000524295.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.797
• Publications: 3 publications found

Genes affected

LINC01933 (HGNC:52756): (long intergenic non-protein coding RNA 1933)

ENSG00000293808 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 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
LINC01933	ENST00000524295.5	n.94-137C>T		intron_variant	Intron 1 of 6	2
ENSG00000293808	ENST00000719158.1	n.242+3042C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31328 AN: 152068 Hom.: 3807 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.212

GnomAD4 exome AF: 0.318 AC: 7 AN: 22 Hom.: 1 AF XY: 0.250 AC XY: 4 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.333 AC: 6 AN: 18

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.206 AC: 31340 AN: 152186 Hom.: 3810 Cov.: 33 AF XY: 0.201 AC XY: 14930 AN XY: 74408

African (AFR) AF: 0.115 AC: 4784 AN: 41526

American (AMR) AF: 0.173 AC: 2652 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 998 AN: 3470

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5180

South Asian (SAS) AF: 0.110 AC: 533 AN: 4824

European-Finnish (FIN) AF: 0.261 AC: 2761 AN: 10576

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18847 AN: 68000

Other (OTH) AF: 0.209 AC: 440 AN: 2106

Alfa AF: 0.251 Hom.: 3572

Bravo AF: 0.195

Asia WGS AF: 0.0680 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.60
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs4958287; hg19: chr5-151330398;