rs366839

Variant names:

• chr1-189589536-G-A
• rs366839
• ENST00000758530.1:n.68-13947G>A

Variant summary

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

The ENST00000758530.1(LINC01701):​n.68-13947G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 151,818 control chromosomes in the GnomAD database, including 23,972 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 0.55 (23972 hom., cov: 31)
• Consequence: LINC01701 ENST00000758530.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 3 publications found

Genes affected

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

LOC105371657 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371657	XR_002958413.2	n.550-13947G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01701	ENST00000758530.1	n.68-13947G>A		intron_variant	Intron 1 of 3
LINC01701	ENST00000758531.1	n.160-13947G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83532 AN: 151700 Hom.: 23941 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.551 AC: 83609 AN: 151818 Hom.: 23972 Cov.: 31 AF XY: 0.546 AC XY: 40503 AN XY: 74176

African (AFR) AF: 0.719 AC: 29793 AN: 41426

American (AMR) AF: 0.439 AC: 6683 AN: 15232

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

East Asian (EAS) AF: 0.455 AC: 2342 AN: 5144

South Asian (SAS) AF: 0.391 AC: 1879 AN: 4806

European-Finnish (FIN) AF: 0.546 AC: 5755 AN: 10542

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33763 AN: 67890

Other (OTH) AF: 0.522 AC: 1098 AN: 2102

Alfa AF: 0.506 Hom.: 25574

Bravo AF: 0.553

Asia WGS AF: 0.441 AC: 1535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.17
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs366839; hg19: chr1-189558666; COSMIC: COSV60002297;