chr5-106843207-C-T

Variant names:

• chr5-106843207-C-T
• rs17159152
• ENST00000505997.2:n.260+854G>A

Variant summary

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

The ENST00000505997.2(LINC01950):​n.260+854G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 151,816 control chromosomes in the GnomAD database, including 4,603 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 0.23 (4603 hom., cov: 31)
• Consequence: LINC01950 ENST00000505997.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 3 publications found

Genes affected

LINC01950 (HGNC:52773): (long intergenic non-protein coding RNA 1950)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01950	NR_104671.1	n.144-24730G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01950	ENST00000505997.2	n.260+854G>A		intron_variant	Intron 2 of 2	3
LINC01950	ENST00000513273.1	n.144-24730G>A		intron_variant	Intron 2 of 3	2
LINC01950	ENST00000657922.2	n.201-24730G>A		intron_variant	Intron 2 of 3
LINC01950	ENST00000661979.1	n.114-24730G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35588 AN: 151698 Hom.: 4601 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.235 AC: 35606 AN: 151816 Hom.: 4603 Cov.: 31 AF XY: 0.236 AC XY: 17526 AN XY: 74166

African (AFR) AF: 0.111 AC: 4599 AN: 41432

American (AMR) AF: 0.260 AC: 3967 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3466

East Asian (EAS) AF: 0.359 AC: 1838 AN: 5124

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4810

European-Finnish (FIN) AF: 0.246 AC: 2590 AN: 10516

Middle Eastern (MID) AF: 0.252 AC: 73 AN: 290

European-Non Finnish (NFE) AF: 0.283 AC: 19226 AN: 67912

Other (OTH) AF: 0.257 AC: 540 AN: 2102

Alfa AF: 0.267 Hom.: 1916

Bravo AF: 0.228

Asia WGS AF: 0.310 AC: 1078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.47
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs17159152; hg19: chr5-106178908;