rs1040988

Variant names:

• chr13-27403163-G-T
• rs1040988
• ENST00000833686.1:n.90-1103G>T

Variant summary

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

The ENST00000833686.1(LINC01079):​n.90-1103G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,094 control chromosomes in the GnomAD database, including 12,955 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 0.40 (12955 hom., cov: 33)
• Consequence: LINC01079 ENST00000833686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 1 publications found

Genes affected

LINC01079 (HGNC:49122): (long intergenic non-protein coding RNA 1079)

LOC124903138 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903138	XR_007063733.1	n.-51G>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01079	ENST00000833686.1	n.90-1103G>T		intron_variant	Intron 1 of 2
LINC01079	ENST00000833687.1	n.593-167G>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61258 AN: 151976 Hom.: 12955 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.403 AC: 61278 AN: 152094 Hom.: 12955 Cov.: 33 AF XY: 0.400 AC XY: 29757 AN XY: 74328

African (AFR) AF: 0.320 AC: 13260 AN: 41462

American (AMR) AF: 0.323 AC: 4932 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1852 AN: 3472

East Asian (EAS) AF: 0.214 AC: 1109 AN: 5182

South Asian (SAS) AF: 0.552 AC: 2661 AN: 4824

European-Finnish (FIN) AF: 0.424 AC: 4474 AN: 10554

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31629 AN: 68002

Other (OTH) AF: 0.417 AC: 880 AN: 2112

Alfa AF: 0.425 Hom.: 1840

Bravo AF: 0.384

Asia WGS AF: 0.394 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs1040988; hg19: chr13-27977300;