14-97940088-A-T

Variant names:

• chr14-97940088-A-T
• rs2809115
• ENST00000499006.8:n.436-13444T>A

Variant summary

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

The ENST00000499006.8(LINC01550):​n.436-13444T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,020 control chromosomes in the GnomAD database, including 24,563 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 0.55 (24563 hom., cov: 32)
• Consequence: LINC01550 ENST00000499006.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 4 publications found

Genes affected

LINC01550 (HGNC:20111): (long intergenic non-protein coding RNA 1550)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01550	NR_015430.2	n.424-13444T>A		intron_variant	Intron 2 of 2
LINC01550	NR_152749.1	n.424-5207T>A		intron_variant	Intron 2 of 2
LINC01550	NR_152750.1	n.347-5207T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01550	ENST00000499006.8	n.436-13444T>A		intron_variant	Intron 2 of 2	1
LINC01550	ENST00000556462.1	n.279-5207T>A		intron_variant	Intron 2 of 2	2
LINC01550	ENST00000652825.1	n.365-5207T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84159 AN: 151902 Hom.: 24509 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.554 AC: 84277 AN: 152020 Hom.: 24563 Cov.: 32 AF XY: 0.557 AC XY: 41412 AN XY: 74284

African (AFR) AF: 0.717 AC: 29722 AN: 41466

American (AMR) AF: 0.594 AC: 9072 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1830 AN: 3472

East Asian (EAS) AF: 0.706 AC: 3646 AN: 5162

South Asian (SAS) AF: 0.645 AC: 3100 AN: 4806

European-Finnish (FIN) AF: 0.464 AC: 4903 AN: 10556

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30278 AN: 67968

Other (OTH) AF: 0.567 AC: 1200 AN: 2116

Alfa AF: 0.495 Hom.: 2415

Bravo AF: 0.566

Asia WGS AF: 0.706 AC: 2452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.76
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2809115; hg19: chr14-98406425;