14-46367909-C-T

Variant names:

• chr14-46367909-C-T
• rs2415974
• ENST00000555246.5:n.299+49048C>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+49048C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,122 control chromosomes in the GnomAD database, including 23,059 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 0.53 (23059 hom., cov: 32)
• Consequence: LINC00871 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00871	NR_102701.1	n.233-70272C>T		intron_variant	Intron 3 of 5
LINC00871	NR_102702.1	n.233-133398C>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+49048C>T		intron_variant	Intron 4 of 5	5
LINC00871	ENST00000556886.1	n.233-70272C>T		intron_variant	Intron 3 of 5	3
LINC00871	ENST00000656720.1	n.234-133398C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80512 AN: 152004 Hom.: 23046 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.530 AC: 80557 AN: 152122 Hom.: 23059 Cov.: 32 AF XY: 0.536 AC XY: 39860 AN XY: 74352

African (AFR) AF: 0.326 AC: 13517 AN: 41510

American (AMR) AF: 0.695 AC: 10621 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2097 AN: 3470

East Asian (EAS) AF: 0.970 AC: 5001 AN: 5156

South Asian (SAS) AF: 0.664 AC: 3206 AN: 4828

European-Finnish (FIN) AF: 0.543 AC: 5745 AN: 10584

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38521 AN: 67980

Other (OTH) AF: 0.568 AC: 1201 AN: 2114

Alfa AF: 0.556 Hom.: 4275

Bravo AF: 0.534

Asia WGS AF: 0.791 AC: 2749 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	3.6
DANN	Benign	0.60
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2415974; hg19: chr14-46837112;