chr1-189761918-A-G

Variant names:

• chr1-189761918-A-G
• rs12132519
• ENST00000419614.2:n.122-5314A>G

Variant summary

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

The ENST00000419614.2(LINC01701):​n.122-5314A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,970 control chromosomes in the GnomAD database, including 15,864 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 0.45 (15864 hom., cov: 32)
• Consequence: LINC01701 ENST00000419614.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 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.122-5314A>G		intron_variant	Intron 1 of 5	2
LINC01701	ENST00000758528.1	n.244-13547A>G		intron_variant	Intron 2 of 4
LINC01701	ENST00000758529.1	n.97+7020A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68836 AN: 151852 Hom.: 15857 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.453 AC: 68868 AN: 151970 Hom.: 15864 Cov.: 32 AF XY: 0.450 AC XY: 33427 AN XY: 74258

African (AFR) AF: 0.446 AC: 18486 AN: 41428

American (AMR) AF: 0.362 AC: 5528 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3468

East Asian (EAS) AF: 0.410 AC: 2115 AN: 5162

South Asian (SAS) AF: 0.385 AC: 1852 AN: 4814

European-Finnish (FIN) AF: 0.524 AC: 5526 AN: 10554

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32280 AN: 67960

Other (OTH) AF: 0.422 AC: 893 AN: 2116

Alfa AF: 0.464 Hom.: 8536

Bravo AF: 0.442

Asia WGS AF: 0.401 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.77
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs12132519; hg19: chr1-189731048; COSMIC: COSV60003618;