14-45998628-A-G

Variant names:

• chr14-45998628-A-G
• rs17728971
• ENST00000555246.5:n.76+57610A>G

Variant summary

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

The ENST00000555246.5(LINC00871):​n.76+57610A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,938 control chromosomes in the GnomAD database, including 12,795 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 0.39 (12795 hom., cov: 32)
• Consequence: LINC00871 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.05
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00871	ENST00000555246.5	TSL:5	n.76+57610A>G		intron	N/A
	LINC00871	ENST00000664642.1		n.185+57610A>G		intron	N/A
	LINC00871	ENST00000666179.1		n.176+57610A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58496 AN: 151820 Hom.: 12786 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.385 AC: 58515 AN: 151938 Hom.: 12795 Cov.: 32 AF XY: 0.383 AC XY: 28459 AN XY: 74286

African (AFR) AF: 0.182 AC: 7538 AN: 41482

American (AMR) AF: 0.388 AC: 5921 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1288 AN: 5164

South Asian (SAS) AF: 0.384 AC: 1848 AN: 4810

European-Finnish (FIN) AF: 0.463 AC: 4891 AN: 10556

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33829 AN: 67898

Other (OTH) AF: 0.413 AC: 868 AN: 2104

Alfa AF: 0.417 Hom.: 1740

Bravo AF: 0.371

Asia WGS AF: 0.310 AC: 1079 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.73
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs17728971; hg19: chr14-46467831;