chr14-50100164-G-A

Variant names:

• chr14-50100164-G-A
• rs7157296
• ENST00000603228.3:n.106+4833C>T

Variant summary

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

The ENST00000603228.3(LINC01588):​n.106+4833C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,940 control chromosomes in the GnomAD database, including 9,168 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 0.34 (9168 hom., cov: 31)
• Consequence: LINC01588 ENST00000603228.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01599	NR_131171.1	n.47+4833C>T		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01588	ENST00000603228.3	n.106+4833C>T		intron_variant	Intron 1 of 8	5
LINC01588	ENST00000685750.2	n.106+4833C>T		intron_variant	Intron 1 of 3
LINC01588	ENST00000769199.1	n.112+4833C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51804 AN: 151822 Hom.: 9155 Cov.: 31

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.341 AC: 51850 AN: 151940 Hom.: 9168 Cov.: 31 AF XY: 0.341 AC XY: 25304 AN XY: 74236

African (AFR) AF: 0.403 AC: 16684 AN: 41374

American (AMR) AF: 0.427 AC: 6526 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1156 AN: 3464

East Asian (EAS) AF: 0.247 AC: 1276 AN: 5174

South Asian (SAS) AF: 0.207 AC: 999 AN: 4818

European-Finnish (FIN) AF: 0.311 AC: 3281 AN: 10546

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20865 AN: 67978

Other (OTH) AF: 0.340 AC: 716 AN: 2108

Alfa AF: 0.340 Hom.: 3937

Bravo AF: 0.357

Asia WGS AF: 0.259 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.65
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs7157296; hg19: chr14-50566882;