chr14-46413069-G-A

Variant names:

• chr14-46413069-G-A
• rs8019899
• ENST00000555246.5:n.300-33116G>A

Variant summary

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

The ENST00000555246.5(LINC00871):​n.300-33116G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,936 control chromosomes in the GnomAD database, including 23,542 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 0.54 (23542 hom., cov: 32)
• Consequence: LINC00871 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00871	NR_102701.1	n.233-25112G>A		intron_variant	Intron 3 of 5
LINC00871	NR_102702.1	n.233-88238G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000555246.5	n.300-33116G>A		intron_variant	Intron 4 of 5	5
LINC00871	ENST00000556886.1	n.233-25112G>A		intron_variant	Intron 3 of 5	3
LINC00871	ENST00000656720.1	n.234-88238G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81617 AN: 151818 Hom.: 23523 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.538 AC: 81671 AN: 151936 Hom.: 23542 Cov.: 32 AF XY: 0.545 AC XY: 40469 AN XY: 74268

African (AFR) AF: 0.346 AC: 14317 AN: 41424

American (AMR) AF: 0.695 AC: 10604 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2074 AN: 3464

East Asian (EAS) AF: 0.969 AC: 5011 AN: 5172

South Asian (SAS) AF: 0.686 AC: 3311 AN: 4824

European-Finnish (FIN) AF: 0.547 AC: 5773 AN: 10556

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38720 AN: 67940

Other (OTH) AF: 0.576 AC: 1210 AN: 2100

Alfa AF: 0.498 Hom.: 2695

Bravo AF: 0.541

Asia WGS AF: 0.807 AC: 2804 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.64
DANN	Benign	0.74
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs8019899; hg19: chr14-46882272;