14-47891810-C-T

Variant names:

• chr14-47891810-C-T
• rs12893288
• ENST00000802535.1:n.243+8814G>A

Variant summary

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

The ENST00000802535.1(LINC00648):​n.243+8814G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 151,898 control chromosomes in the GnomAD database, including 3,927 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 0.21 (3927 hom., cov: 33)
• Consequence: LINC00648 ENST00000802535.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 2 publications found

Genes affected

LINC00648 (HGNC:44302): (long intergenic non-protein coding RNA 648)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00648	ENST00000802535.1	n.243+8814G>A		intron_variant	Intron 2 of 3
LINC00648	ENST00000802536.1	n.129+9716G>A		intron_variant	Intron 1 of 2
LINC00648	ENST00000802537.1	n.239+8814G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31471 AN: 151780 Hom.: 3917 Cov.: 33

Gnomad AFR AF: 0.0652

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.207 AC: 31498 AN: 151898 Hom.: 3927 Cov.: 33 AF XY: 0.216 AC XY: 16015 AN XY: 74186

African (AFR) AF: 0.0651 AC: 2702 AN: 41474

American (AMR) AF: 0.252 AC: 3846 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3466

East Asian (EAS) AF: 0.392 AC: 2017 AN: 5148

South Asian (SAS) AF: 0.335 AC: 1612 AN: 4808

European-Finnish (FIN) AF: 0.270 AC: 2835 AN: 10500

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17030 AN: 67934

Other (OTH) AF: 0.233 AC: 491 AN: 2104

Alfa AF: 0.224 Hom.: 721

Bravo AF: 0.198

Asia WGS AF: 0.399 AC: 1379 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
DANN	Benign	0.12
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs12893288; hg19: chr14-48361013;