chr14-46239055-A-T

Variant names:

• chr14-46239055-A-T
• rs10483595
• ENST00000555246.5:n.250+27251A>T

Variant summary

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

The ENST00000555246.5(LINC00871):​n.250+27251A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0425 in 152,176 control chromosomes in the GnomAD database, including 275 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 0.042 (275 hom., cov: 32)
• Consequence: LINC00871 ENST00000555246.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00871	NR_102701.1	n.232+27251A>T		intron_variant	Intron 3 of 5
LINC00871	NR_102702.1	n.232+27251A>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00871	ENST00000555246.5	n.250+27251A>T		intron_variant	Intron 3 of 5	5
LINC00871	ENST00000556886.1	n.232+27251A>T		intron_variant	Intron 3 of 5	3
LINC00871	ENST00000656720.1	n.233+27251A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0425 AC: 6458 AN: 152058 Hom.: 272 Cov.: 32

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0318

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0484

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0425 AC: 6464 AN: 152176 Hom.: 275 Cov.: 32 AF XY: 0.0435 AC XY: 3238 AN XY: 74418

African (AFR) AF: 0.0103 AC: 430 AN: 41554

American (AMR) AF: 0.0395 AC: 602 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0318 AC: 110 AN: 3464

East Asian (EAS) AF: 0.178 AC: 923 AN: 5178

South Asian (SAS) AF: 0.146 AC: 704 AN: 4822

European-Finnish (FIN) AF: 0.0202 AC: 214 AN: 10614

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0484 AC: 3292 AN: 67966

Other (OTH) AF: 0.0534 AC: 113 AN: 2116

Alfa AF: 0.0421 Hom.: 19

Bravo AF: 0.0403

Asia WGS AF: 0.132 AC: 461 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.45
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs10483595; hg19: chr14-46708258;