rs1938516

Variant names:

• chr1-187433789-T-A
• rs1938516
• ENST00000609113.3:n.714-9839T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643891.1. 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.714-9839T>A		intron	N/A
	LINC01036	ENST00000643891.1		n.1070-9839T>A		intron	N/A
	LINC01036	ENST00000644419.2		n.322-9839T>A		intron	N/A

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

African (AFR) AF: 0.144 AC: 5957 AN: 41468

American (AMR) AF: 0.0255 AC: 390 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3472

East Asian (EAS) AF: 0.149 AC: 768 AN: 5164

South Asian (SAS) AF: 0.0719 AC: 347 AN: 4824

European-Finnish (FIN) AF: 0.0240 AC: 255 AN: 10618

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0126 AC: 855 AN: 68018

Other (OTH) AF: 0.0497 AC: 105 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.37
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1938516; hg19: chr1-187402921;