rs1993434

Variant names:

• chr9-103272026-A-G
• rs1993434
• ENST00000411575.5:n.645+4005T>C

Variant summary

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

The ENST00000411575.5(LINC01492):​n.645+4005T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,664 control chromosomes in the GnomAD database, including 11,240 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 0.37 (11240 hom., cov: 31)
• Consequence: LINC01492 ENST00000411575.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 1 publications found

Genes affected

LINC01492 (HGNC:51149): (long intergenic non-protein coding RNA 1492)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411575.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01492	NR_121578.1		n.644+4005T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01492	ENST00000411575.5	TSL:1	n.645+4005T>C		intron	N/A
	LINC01492	ENST00000806271.1		n.289-7376T>C		intron	N/A
	LINC01492	ENST00000806272.1		n.424-7376T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56823 AN: 151546 Hom.: 11231 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.375 AC: 56862 AN: 151664 Hom.: 11240 Cov.: 31 AF XY: 0.372 AC XY: 27559 AN XY: 74076

African (AFR) AF: 0.268 AC: 11074 AN: 41380

American (AMR) AF: 0.358 AC: 5441 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1391 AN: 3460

East Asian (EAS) AF: 0.206 AC: 1052 AN: 5104

South Asian (SAS) AF: 0.315 AC: 1514 AN: 4806

European-Finnish (FIN) AF: 0.464 AC: 4869 AN: 10494

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30107 AN: 67912

Other (OTH) AF: 0.370 AC: 778 AN: 2104

Alfa AF: 0.418 Hom.: 2761

Bravo AF: 0.366

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.66
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1993434; hg19: chr9-106034308;