chr14-88021345-C-A

Variant names:

• chr14-88021345-C-A
• rs2119704
• ENST00000553921.1:n.368+2330G>T

Variant summary

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

The ENST00000553921.1(LINC01147):​n.368+2330G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,158 control chromosomes in the GnomAD database, including 1,311 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 0.11 (1311 hom., cov: 32)
• Consequence: LINC01147 ENST00000553921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 53 publications found

Genes affected

LINC01147 (HGNC:49468): (long intergenic non-protein coding RNA 1147)

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 (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01147	NR_110121.1	n.327+2330G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01147	ENST00000553921.1	n.368+2330G>T		intron_variant	Intron 4 of 4	3
LINC01147	ENST00000557631.6	n.349+2330G>T		intron_variant	Intron 2 of 2	3
LINC01147	ENST00000716957.1	n.328+2330G>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17183 AN: 152040 Hom.: 1311 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0617

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0470

Gnomad FIN AF: 0.0616

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.113 AC: 17203 AN: 152158 Hom.: 1311 Cov.: 32 AF XY: 0.111 AC XY: 8239 AN XY: 74402

African (AFR) AF: 0.203 AC: 8421 AN: 41490

American (AMR) AF: 0.0616 AC: 942 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1002 AN: 5158

South Asian (SAS) AF: 0.0475 AC: 229 AN: 4824

European-Finnish (FIN) AF: 0.0616 AC: 653 AN: 10604

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0791 AC: 5378 AN: 67998

Other (OTH) AF: 0.109 AC: 231 AN: 2112

Alfa AF: 0.0883 Hom.: 3374

Bravo AF: 0.119

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.76
DANN	Benign	0.61
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2119704; hg19: chr14-88487689;