rs7543130

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 29 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635551.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01708	ENST00000635551.1	TSL:5	n.163+16083G>T		intron	N/A

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

African (AFR) AF: 0.236 AC: 9782 AN: 41452

American (AMR) AF: 0.309 AC: 4714 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1457 AN: 3464

East Asian (EAS) AF: 0.0540 AC: 279 AN: 5170

South Asian (SAS) AF: 0.239 AC: 1150 AN: 4812

European-Finnish (FIN) AF: 0.463 AC: 4884 AN: 10548

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34219 AN: 67918

Other (OTH) AF: 0.408 AC: 861 AN: 2110

Alfa AF: 0.448 Hom.: 58426

Bravo AF: 0.362

Asia WGS AF: 0.154 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		-0.044

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7543130;

hg19: chr1-100049785;