rs1951319

chr14-45970841-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000666179.1(LINC00871):n.176+29823G>T variant causes a intron, non coding transcript 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 ENST00000666179.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00871	ENST00000666179.1	n.176+29823G>T		intron_variant, non_coding_transcript_variant
LINC00871	ENST00000555246.5	n.76+29823G>T		intron_variant, non_coding_transcript_variant		5
LINC00871	ENST00000664642.1	n.185+29823G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.441

Alfa AF: 0.450 Hom.: 1970

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1951319; hg19: chr14-46440044;