14-45970841-G-T

Variant names:

• chr14-45970841-G-T
• rs1951319
• ENST00000555246.5:n.76+29823G>T

Variant summary

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

The ENST00000555246.5(LINC00871):​n.76+29823G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,590 control chromosomes in the GnomAD database, including 14,390 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 0.43 (14390 hom., cov: 33)
• Consequence: LINC00871 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000555246.5	n.76+29823G>T		intron_variant	Intron 1 of 5	5
LINC00871	ENST00000664642.1	n.185+29823G>T		intron_variant	Intron 2 of 5
LINC00871	ENST00000666179.1	n.176+29823G>T		intron_variant	Intron 2 of 4
LINC00871	ENST00000761148.1	n.180-27025G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64548 AN: 151470 Hom.: 14377 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.426 AC: 64580 AN: 151590 Hom.: 14390 Cov.: 33 AF XY: 0.422 AC XY: 31246 AN XY: 74046

African (AFR) AF: 0.326 AC: 13485 AN: 41402

American (AMR) AF: 0.400 AC: 6091 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1550 AN: 3460

East Asian (EAS) AF: 0.246 AC: 1256 AN: 5104

South Asian (SAS) AF: 0.385 AC: 1856 AN: 4822

European-Finnish (FIN) AF: 0.465 AC: 4895 AN: 10536

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33736 AN: 67746

Other (OTH) AF: 0.441 AC: 928 AN: 2106

Alfa AF: 0.445 Hom.: 2003

Bravo AF: 0.417

Asia WGS AF: 0.321 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.37
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1951319; hg19: chr14-46440044;