chr14-46343258-C-T

Variant names:

• chr14-46343258-C-T
• rs12437159
• ENST00000555246.5:n.299+24397C>T

Variant summary

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

The ENST00000555246.5(LINC00871):​n.299+24397C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,766 control chromosomes in the GnomAD database, including 18,598 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 0.47 (18598 hom., cov: 31)
• Consequence: LINC00871 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00871	NR_102701.1	n.233-94923C>T		intron_variant	Intron 3 of 5
LINC00871	NR_102702.1	n.232+131454C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000555246.5	n.299+24397C>T		intron_variant	Intron 4 of 5	5
LINC00871	ENST00000556886.1	n.233-94923C>T		intron_variant	Intron 3 of 5	3
LINC00871	ENST00000656720.1	n.233+131454C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71678 AN: 151648 Hom.: 18585 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.472 AC: 71704 AN: 151766 Hom.: 18598 Cov.: 31 AF XY: 0.477 AC XY: 35389 AN XY: 74176

African (AFR) AF: 0.248 AC: 10249 AN: 41394

American (AMR) AF: 0.663 AC: 10081 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1899 AN: 3466

East Asian (EAS) AF: 0.625 AC: 3209 AN: 5136

South Asian (SAS) AF: 0.577 AC: 2773 AN: 4804

European-Finnish (FIN) AF: 0.483 AC: 5088 AN: 10530

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36682 AN: 67912

Other (OTH) AF: 0.516 AC: 1088 AN: 2110

Alfa AF: 0.531 Hom.: 30364

Bravo AF: 0.476

Asia WGS AF: 0.571 AC: 1983 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.94
DANN	Benign	0.75
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs12437159; hg19: chr14-46812461;