rs1389608

Variant names:

• chr14-46488574-C-A
• rs1389608
• ENST00000556071.5:n.154-1618C>A

Variant summary

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

The ENST00000556869.1(LINC00871):​n.152-12733C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,894 control chromosomes in the GnomAD database, including 10,050 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 0.35 (10050 hom., cov: 33)
• Consequence: LINC00871 ENST00000556869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 3 publications found

Genes affected

LINC00871 (HGNC:47038): (long intergenic non-protein coding RNA 871)

LOC124903309 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556869.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00871	NR_102699.1		n.154-1618C>A		intron	N/A
	LINC00871	NR_102700.1		n.154-12733C>A		intron	N/A
	LINC00871	NR_102701.1		n.350-12733C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00871	ENST00000556071.5	TSL:3	n.154-1618C>A		intron	N/A
	LINC00871	ENST00000556869.1	TSL:2	n.152-12733C>A		intron	N/A
	LINC00871	ENST00000556886.1	TSL:3	n.350-12733C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52835 AN: 151776 Hom.: 10026 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.0709

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.348 AC: 52881 AN: 151894 Hom.: 10050 Cov.: 33 AF XY: 0.345 AC XY: 25590 AN XY: 74238

African (AFR) AF: 0.284 AC: 11769 AN: 41472

American (AMR) AF: 0.541 AC: 8239 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3466

East Asian (EAS) AF: 0.0707 AC: 363 AN: 5138

South Asian (SAS) AF: 0.296 AC: 1427 AN: 4822

European-Finnish (FIN) AF: 0.274 AC: 2898 AN: 10560

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25522 AN: 67904

Other (OTH) AF: 0.375 AC: 790 AN: 2104

Alfa AF: 0.360 Hom.: 1339

Bravo AF: 0.369

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.53
DANN	Benign	0.43
PhyloP100		-0.40

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1389608;

hg19: chr14-46957777;