rs10067788

Variant names:

• chr5-151953450-A-C
• rs10067788
• ENST00000524295.5:n.199+1770A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000524295.5(LINC01933):​n.199+1770A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,062 control chromosomes in the GnomAD database, including 3,658 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 0.17 (3658 hom., cov: 32)
• Consequence: LINC01933 ENST00000524295.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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.199+1770A>C		intron_variant	Intron 3 of 6	2

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25468 AN: 151944 Hom.: 3643 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.0817

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0355

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0719

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.168 AC: 25516 AN: 152062 Hom.: 3658 Cov.: 32 AF XY: 0.165 AC XY: 12234 AN XY: 74340

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.0164

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.0355

Gnomad4 NFE AF: 0.0720

Gnomad4 OTH AF: 0.154

Alfa AF: 0.0925 Hom.: 1723

Bravo AF: 0.186

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10067788; hg19: chr5-151333011;