14-46488574-C-A

Position:

• chr14-46488574-C-A

Variant summary

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

The NR_102701.1(LINC00871):​n.350-12733C>A 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 0.348 in 151,894 control chromosomes in the GnomAD database, including 10,050 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 0.35 (10050 hom., cov: 33)
• Consequence: LINC00871 NR_102701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

Genes affected

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

LOC124903309 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00871	NR_102701.1	n.350-12733C>A		intron_variant, non_coding_transcript_variant
LOC124903309	XR_007064146.1	n.2465-358G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000666179.1	n.351-12733C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52835 AN: 151776 Hom.: 10026 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.0709

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.348 AC: 52881 AN: 151894 Hom.: 10050 Cov.: 33 AF XY: 0.345 AC XY: 25590 AN XY: 74238

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.0707

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.375

Alfa AF: 0.362 Hom.: 1310

Bravo AF: 0.369

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.53
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1389608; hg19: chr14-46957777;