rs7543130

Variant names:

• chr1-99584229-C-A
• rs7543130
• ENST00000635551.1:n.163+16083G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635551.1(LINC01708):​n.163+16083G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,954 control chromosomes in the GnomAD database, including 12,634 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 0.38 (12634 hom., cov: 31)
• Consequence: LINC01708 ENST00000635551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

Genes affected

LINC01708 (HGNC:52496): (long intergenic non-protein coding RNA 1708)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 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
LINC01708	ENST00000635551.1	n.163+16083G>T		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57996 AN: 151836 Hom.: 12636 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.0542

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.382 AC: 57989 AN: 151954 Hom.: 12634 Cov.: 31 AF XY: 0.373 AC XY: 27682 AN XY: 74262

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.309

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.0540

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.408

Alfa AF: 0.466 Hom.: 39184

Bravo AF: 0.362

Asia WGS AF: 0.154 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7543130; hg19: chr1-100049785;