rs155908

Variant names:

• chr1-189604414-G-A
• rs155908
• ENST00000758530.1:n.208-684G>A

Variant summary

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

The ENST00000758530.1(LINC01701):​n.208-684G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,790 control chromosomes in the GnomAD database, including 24,886 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 0.56 (24886 hom., cov: 32)
• Consequence: LINC01701 ENST00000758530.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53
• Publications: 2 publications found

Genes affected

LINC01701 (HGNC:52489): (long intergenic non-protein coding RNA 1701)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 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
LINC01701	ENST00000758530.1	n.208-684G>A		intron_variant	Intron 2 of 3
LINC01701	ENST00000758531.1	n.300-684G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84762 AN: 151674 Hom.: 24856 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.559 AC: 84838 AN: 151790 Hom.: 24886 Cov.: 32 AF XY: 0.554 AC XY: 41105 AN XY: 74148

African (AFR) AF: 0.747 AC: 30989 AN: 41458

American (AMR) AF: 0.442 AC: 6723 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1644 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2353 AN: 5162

South Asian (SAS) AF: 0.390 AC: 1878 AN: 4812

European-Finnish (FIN) AF: 0.546 AC: 5752 AN: 10540

Middle Eastern (MID) AF: 0.472 AC: 135 AN: 286

European-Non Finnish (NFE) AF: 0.497 AC: 33735 AN: 67830

Other (OTH) AF: 0.528 AC: 1115 AN: 2112

Alfa AF: 0.539 Hom.: 2945

Bravo AF: 0.562

Asia WGS AF: 0.436 AC: 1513 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.083
DANN	Benign	0.36
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs155908; hg19: chr1-189573544;