1-99584229-C-A

Position:

• chr1-99584229-C-A

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01708	ENST00000635551.1	n.163+16083G>T		intron_variant, non_coding_transcript_variant		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;