14-50049996-T-C

Variant names:

• chr14-50049996-T-C
• rs11157721
• ENST00000556019.2:n.187-2407A>G

Variant summary

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

The ENST00000556019.2(LINC01588):​n.187-2407A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 152,100 control chromosomes in the GnomAD database, including 21,076 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 0.50 (21076 hom., cov: 32)
• Consequence: LINC01588 ENST00000556019.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01599	NR_131171.1	n.254-2407A>G		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01588	ENST00000556019.2	n.187-2407A>G		intron_variant	Intron 2 of 4	3
LINC01588	ENST00000557142.6	n.2566+2778A>G		intron_variant	Intron 2 of 6	3
LINC01588	ENST00000603228.3	n.313-2407A>G		intron_variant	Intron 3 of 8	5
LINC01588	ENST00000635379.1	n.215-2407A>G		intron_variant	Intron 2 of 11	5

Frequencies

GnomAD3 genomes AF: 0.500 AC: 76010 AN: 151982 Hom.: 21074 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.500 AC: 76019 AN: 152100 Hom.: 21076 Cov.: 32 AF XY: 0.501 AC XY: 37269 AN XY: 74340

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.499

Alfa AF: 0.591 Hom.: 54644

Bravo AF: 0.483

Asia WGS AF: 0.527 AC: 1832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.044
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11157721; hg19: chr14-50516714;