1-189754493-A-G

Variant names:

• chr1-189754493-A-G
• rs10737562
• ENST00000419614.2:n.121+8830A>G

Variant summary

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

The ENST00000419614.2(LINC01701):​n.121+8830A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,032 control chromosomes in the GnomAD database, including 24,307 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 (24307 hom., cov: 32)
• Consequence: LINC01701 ENST00000419614.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797
• Publications: 11 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 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	ENST00000419614.2	n.121+8830A>G		intron_variant	Intron 1 of 5	2
LINC01701	ENST00000758528.1	n.243+8830A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83917 AN: 151916 Hom.: 24284 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.552 AC: 83984 AN: 152032 Hom.: 24307 Cov.: 32 AF XY: 0.547 AC XY: 40666 AN XY: 74316

African (AFR) AF: 0.733 AC: 30385 AN: 41470

American (AMR) AF: 0.450 AC: 6874 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1698 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2116 AN: 5146

South Asian (SAS) AF: 0.411 AC: 1985 AN: 4824

European-Finnish (FIN) AF: 0.527 AC: 5568 AN: 10560

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33610 AN: 67966

Other (OTH) AF: 0.515 AC: 1086 AN: 2110

Alfa AF: 0.516 Hom.: 35070

Bravo AF: 0.558

Asia WGS AF: 0.440 AC: 1532 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.48
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs10737562; hg19: chr1-189723623;