14-46155176-A-G

Variant names:

• chr14-46155176-A-G
• rs751147
• ENST00000555246.5:n.77-55648A>G

Variant summary

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

The ENST00000555246.5(LINC00871):​n.77-55648A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,700 control chromosomes in the GnomAD database, including 28,791 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 0.59 (28791 hom., cov: 31)
• Consequence: LINC00871 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 2 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555246.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00871	NR_102701.1		n.59-55648A>G		intron	N/A
	LINC00871	NR_102702.1		n.59-55648A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00871	ENST00000555246.5	TSL:5	n.77-55648A>G		intron	N/A
	LINC00871	ENST00000556886.1	TSL:3	n.59-55648A>G		intron	N/A
	LINC00871	ENST00000656720.1		n.60-55648A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89292 AN: 151582 Hom.: 28773 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.589 AC: 89337 AN: 151700 Hom.: 28791 Cov.: 31 AF XY: 0.597 AC XY: 44230 AN XY: 74134

African (AFR) AF: 0.316 AC: 13080 AN: 41358

American (AMR) AF: 0.743 AC: 11283 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2583 AN: 3468

East Asian (EAS) AF: 0.428 AC: 2194 AN: 5124

South Asian (SAS) AF: 0.599 AC: 2884 AN: 4816

European-Finnish (FIN) AF: 0.759 AC: 8024 AN: 10570

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47258 AN: 67864

Other (OTH) AF: 0.624 AC: 1316 AN: 2110

Alfa AF: 0.675 Hom.: 28489

Bravo AF: 0.578

Asia WGS AF: 0.529 AC: 1837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs751147; hg19: chr14-46624379;