chr14-97973143-C-T

Variant names:

• chr14-97973143-C-T
• rs2776601
• ENST00000499006.8:n.161-3596G>A

Variant summary

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

The ENST00000499006.8(LINC01550):​n.161-3596G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,892 control chromosomes in the GnomAD database, including 11,322 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 0.38 (11322 hom., cov: 32)
• Consequence: LINC01550 ENST00000499006.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01550	NR_015430.2	n.149-3596G>A		intron_variant	Intron 1 of 2
LINC01550	NR_152746.1	n.149-3596G>A		intron_variant	Intron 1 of 3
LINC01550	NR_152747.1	n.149-3596G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01550	ENST00000499006.8	n.161-3596G>A		intron_variant	Intron 1 of 2	1
LINC01550	ENST00000512901.6	n.133-3596G>A		intron_variant	Intron 1 of 2	1
LINC01550	ENST00000736874.1	n.247G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57352 AN: 151776 Hom.: 11299 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.317

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.378 AC: 57423 AN: 151892 Hom.: 11322 Cov.: 32 AF XY: 0.388 AC XY: 28758 AN XY: 74214

African (AFR) AF: 0.385 AC: 15973 AN: 41442

American (AMR) AF: 0.459 AC: 7012 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3472

East Asian (EAS) AF: 0.580 AC: 2979 AN: 5132

South Asian (SAS) AF: 0.504 AC: 2415 AN: 4796

European-Finnish (FIN) AF: 0.438 AC: 4614 AN: 10536

Middle Eastern (MID) AF: 0.324 AC: 94 AN: 290

European-Non Finnish (NFE) AF: 0.326 AC: 22139 AN: 67938

Other (OTH) AF: 0.377 AC: 797 AN: 2112

Alfa AF: 0.353 Hom.: 1276

Bravo AF: 0.378

Asia WGS AF: 0.564 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.9
DANN	Benign	0.30
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2776601; hg19: chr14-98439480;