rs12147964

Variant names:

• chr14-46349819-G-C
• rs12147964
• ENST00000555246.5:n.299+30958G>C

Variant summary

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

The ENST00000555246.5(LINC00871):​n.299+30958G>C variant causes a intron 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 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• Publications: 4 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 = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00871	NR_102701.1	n.233-88362G>C		intron_variant	Intron 3 of 5
LINC00871	NR_102702.1	n.232+138015G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000555246.5	n.299+30958G>C		intron_variant	Intron 4 of 5	5
LINC00871	ENST00000556886.1	n.233-88362G>C		intron_variant	Intron 3 of 5	3
LINC00871	ENST00000656720.1	n.233+138015G>C		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.324 AC: 13419 AN: 41456

American (AMR) AF: 0.266 AC: 4055 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1322 AN: 3464

East Asian (EAS) AF: 0.0298 AC: 154 AN: 5174

South Asian (SAS) AF: 0.334 AC: 1608 AN: 4820

European-Finnish (FIN) AF: 0.458 AC: 4813 AN: 10506

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29320 AN: 67812

Other (OTH) AF: 0.365 AC: 769 AN: 2108

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs12147964; hg19: chr14-46819022;