rs7141809

Variant names:

• chr14-50094227-A-G
• rs7141809
• ENST00000603228.3:n.107-5032T>C

Variant summary

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

The ENST00000603228.3(LINC01588):​n.107-5032T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,056 control chromosomes in the GnomAD database, including 7,929 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 0.30 (7929 hom., cov: 32)
• Consequence: LINC01588 ENST00000603228.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 5 publications found

Genes affected

LINC01588 (HGNC:27503): (long intergenic non-protein coding RNA 1588)

LINC01599 (HGNC:27285): (long intergenic non-protein coding RNA 1599)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01599	NR_131171.1	n.48-5032T>C		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01588	ENST00000603228.3	n.107-5032T>C		intron_variant	Intron 1 of 8	5
LINC01588	ENST00000685750.2	n.107-5032T>C		intron_variant	Intron 1 of 3
LINC01588	ENST00000769199.1	n.112+10770T>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45666 AN: 151938 Hom.: 7927 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.301 AC: 45694 AN: 152056 Hom.: 7929 Cov.: 32 AF XY: 0.298 AC XY: 22140 AN XY: 74320

African (AFR) AF: 0.126 AC: 5227 AN: 41510

American (AMR) AF: 0.258 AC: 3948 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3468

East Asian (EAS) AF: 0.231 AC: 1192 AN: 5160

South Asian (SAS) AF: 0.326 AC: 1571 AN: 4814

European-Finnish (FIN) AF: 0.375 AC: 3959 AN: 10544

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27249 AN: 67956

Other (OTH) AF: 0.316 AC: 666 AN: 2110

Alfa AF: 0.371 Hom.: 6086

Bravo AF: 0.282

Asia WGS AF: 0.248 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	19
DANN	Benign	0.85
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7141809; hg19: chr14-50560945;