chr14-46488719-T-C

Variant names:

• chr14-46488719-T-C
• rs1389607
• ENST00000556071.5:n.154-1473T>C

Variant summary

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

The ENST00000556071.5(LINC00871):​n.154-1473T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 151,690 control chromosomes in the GnomAD database, including 27,856 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 0.60 (27856 hom., cov: 30)
• Consequence: LINC00871 ENST00000556071.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.01
• Publications: 3 publications found

Genes affected

LINC00871 (HGNC:47038): (long intergenic non-protein coding RNA 871)

LOC124903309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.18).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00871	NR_102699.1	n.154-1473T>C		intron_variant	Intron 1 of 2
LINC00871	NR_102700.1	n.154-12588T>C		intron_variant	Intron 1 of 1
LINC00871	NR_102701.1	n.350-12588T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000556071.5	n.154-1473T>C		intron_variant	Intron 1 of 2	3
LINC00871	ENST00000556869.1	n.152-12588T>C		intron_variant	Intron 1 of 1	2
LINC00871	ENST00000556886.1	n.350-12588T>C		intron_variant	Intron 5 of 5	3

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90478 AN: 151572 Hom.: 27848 Cov.: 30

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.597 AC: 90504 AN: 151690 Hom.: 27856 Cov.: 30 AF XY: 0.601 AC XY: 44536 AN XY: 74096

African (AFR) AF: 0.547 AC: 22624 AN: 41380

American (AMR) AF: 0.431 AC: 6548 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1951 AN: 3462

East Asian (EAS) AF: 0.929 AC: 4768 AN: 5130

South Asian (SAS) AF: 0.682 AC: 3279 AN: 4808

European-Finnish (FIN) AF: 0.725 AC: 7649 AN: 10556

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41663 AN: 67856

Other (OTH) AF: 0.585 AC: 1230 AN: 2104

Alfa AF: 0.609 Hom.: 14398

Bravo AF: 0.570

Asia WGS AF: 0.749 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.014
DANN	Benign	0.29
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs1389607; hg19: chr14-46957922;