rs1938516

Variant names:

• chr1-187433789-T-A
• rs1938516
• ENST00000609113.2:n.705-9839T>A

Variant summary

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

The ENST00000643891.1(LINC01036):​n.1070-9839T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0572 in 152,168 control chromosomes in the GnomAD database, including 592 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 0.057 (592 hom., cov: 32)
• Consequence: LINC01036 ENST00000643891.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 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
LINC01036	ENST00000609113.2	n.705-9839T>A		intron_variant	Intron 3 of 4	6
LINC01036	ENST00000643891.1	n.1070-9839T>A		intron_variant	Intron 5 of 8
LINC01036	ENST00000644419.1	n.299-9839T>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8670 AN: 152050 Hom.: 587 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0254

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0719

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0126

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0572 AC: 8701 AN: 152168 Hom.: 592 Cov.: 32 AF XY: 0.0576 AC XY: 4285 AN XY: 74412

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0255

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0719

Gnomad4 FIN AF: 0.0240

Gnomad4 NFE AF: 0.0126

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0373 Hom.: 47

Bravo AF: 0.0612

Asia WGS AF: 0.111 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938516; hg19: chr1-187402921;