ENST00000609113.3:n.714-718A>T

Variant names:

• chr1-187442910-A-T
• rs2244067
• ENST00000609113.3:n.714-718A>T

Variant summary

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

The ENST00000609113.3(LINC01036):​n.714-718A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,938 control chromosomes in the GnomAD database, including 8,475 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 0.31 (8475 hom., cov: 32)
• Consequence: LINC01036 ENST00000609113.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758
• Publications: 4 publications found

Genes affected

LINC01036 (HGNC:49024): (long intergenic non-protein coding RNA 1036)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609113.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01036	ENST00000609113.3	TSL:6	n.714-718A>T		intron	N/A
	LINC01036	ENST00000643891.1		n.1070-718A>T		intron	N/A
	LINC01036	ENST00000644419.2		n.322-718A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47031 AN: 151820 Hom.: 8463 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.310 AC: 47088 AN: 151938 Hom.: 8475 Cov.: 32 AF XY: 0.309 AC XY: 22933 AN XY: 74280

African (AFR) AF: 0.477 AC: 19752 AN: 41410

American (AMR) AF: 0.330 AC: 5028 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3462

East Asian (EAS) AF: 0.504 AC: 2590 AN: 5142

South Asian (SAS) AF: 0.356 AC: 1713 AN: 4810

European-Finnish (FIN) AF: 0.173 AC: 1834 AN: 10588

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14662 AN: 67954

Other (OTH) AF: 0.289 AC: 612 AN: 2114

Alfa AF: 0.260 Hom.: 804

Bravo AF: 0.328

Asia WGS AF: 0.407 AC: 1413 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.52
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs2244067; hg19: chr1-187412042;