1-187442910-A-T

Position:

• chr1-187442910-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000643891.1(LINC01036):​n.1070-718A>T variant causes a intron, non coding transcript 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 ENST00000643891.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01036	ENST00000643891.1	n.1070-718A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.289

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2244067; hg19: chr1-187412042;