14-28780143-T-G

Variant names:

• chr14-28780143-T-G
• rs2038256
• ENST00000399387.9:n.1254+6710T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000399387.9(LINC01551):​n.1254+6710T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 151,970 control chromosomes in the GnomAD database, including 2,770 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 0.18 (2770 hom., cov: 32)
• Consequence: LINC01551 ENST00000399387.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 15 publications found

Genes affected

LINC01551 (HGNC:19828): (long intergenic non-protein coding RNA 1551)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01551	NR_026731.1	n.226+6710T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01551	ENST00000399387.9	n.1254+6710T>G		intron_variant	Intron 2 of 2	1
LINC01551	ENST00000548213.4	n.149+6710T>G		intron_variant	Intron 2 of 2	3
LINC01551	ENST00000622740.3	n.1254+6710T>G		intron_variant	Intron 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26931 AN: 151852 Hom.: 2774 Cov.: 32

Gnomad AFR AF: 0.0928

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.177 AC: 26938 AN: 151970 Hom.: 2770 Cov.: 32 AF XY: 0.184 AC XY: 13663 AN XY: 74258

African (AFR) AF: 0.0927 AC: 3843 AN: 41448

American (AMR) AF: 0.285 AC: 4350 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 790 AN: 3466

East Asian (EAS) AF: 0.111 AC: 571 AN: 5162

South Asian (SAS) AF: 0.285 AC: 1371 AN: 4812

European-Finnish (FIN) AF: 0.261 AC: 2753 AN: 10564

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12584 AN: 67940

Other (OTH) AF: 0.176 AC: 370 AN: 2108

Alfa AF: 0.180 Hom.: 9036

Bravo AF: 0.173

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	16
DANN	Benign	0.76
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2038256; hg19: chr14-29249349;