chr5-151953450-A-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524295.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01933	ENST00000524295.5	TSL:2	n.199+1770A>C		intron	N/A
	ENSG00000293808	ENST00000719158.1		n.242+5655A>C		intron	N/A

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

African (AFR) AF: 0.389 AC: 16097 AN: 41418

American (AMR) AF: 0.151 AC: 2309 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3472

East Asian (EAS) AF: 0.0164 AC: 85 AN: 5174

South Asian (SAS) AF: 0.183 AC: 879 AN: 4814

European-Finnish (FIN) AF: 0.0355 AC: 376 AN: 10602

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0720 AC: 4894 AN: 67992

Other (OTH) AF: 0.154 AC: 326 AN: 2114

Alfa AF: 0.101 Hom.: 2593

Bravo AF: 0.186

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		0.067
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10067788;

hg19: chr5-151333011;