rs12147964

chr14-46349819-G-C

Variant summary

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

The NR_102701.1(LINC00871):n.233-88362G>C 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 0.369 in 151,780 control chromosomes in the GnomAD database, including 10,973 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 0.37 (10973 hom., cov: 32)
• Consequence: LINC00871 NR_102701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319

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 = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00871	NR_102701.1	n.233-88362G>C		intron_variant, non_coding_transcript_variant
LINC00871	NR_102702.1	n.232+138015G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00871	ENST00000666179.1	n.350+138015G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55987 AN: 151662 Hom.: 10972 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.0299

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.369 AC: 56008 AN: 151780 Hom.: 10973 Cov.: 32 AF XY: 0.365 AC XY: 27055 AN XY: 74152

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.0298

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.365

Alfa AF: 0.395 Hom.: 1506

Bravo AF: 0.350

Asia WGS AF: 0.185 AC: 645 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.95
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12147964; hg19: chr14-46819022;