rs2119704

Positions:

• chr14-88021345-C-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC01147 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01147	NR_110121.1	n.327+2330G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01147	ENST00000553921.1	n.368+2330G>T		intron_variant		3
LINC01147	ENST00000557631.6	n.349+2330G>T		intron_variant		3

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

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0616

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.0475

Gnomad4 FIN AF: 0.0616

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0818 Hom.: 1269

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2119704; hg19: chr14-88487689;