rs2040587

Variant names:

• chr7-115035469-G-A
• rs2040587
• ENST00000660905.1:n.244+3644G>A

Variant summary

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

The ENST00000660905.1(LINC01393):​n.244+3644G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 151,926 control chromosomes in the GnomAD database, including 28,598 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 0.61 (28598 hom., cov: 32)
• Consequence: LINC01393 ENST00000660905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522
• Publications: 5 publications found

Genes affected

LINC01393 (HGNC:50669): (long intergenic non-protein coding RNA 1393)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 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
LINC01393	ENST00000660905.1	n.244+3644G>A		intron_variant	Intron 2 of 4
LINC01393	ENST00000668211.1	n.137+3644G>A		intron_variant	Intron 2 of 4
LINC01393	ENST00000669990.1	n.160+3644G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92941 AN: 151810 Hom.: 28582 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.612 AC: 93011 AN: 151926 Hom.: 28598 Cov.: 32 AF XY: 0.615 AC XY: 45655 AN XY: 74256

African (AFR) AF: 0.562 AC: 23298 AN: 41424

American (AMR) AF: 0.582 AC: 8876 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2240 AN: 3466

East Asian (EAS) AF: 0.480 AC: 2482 AN: 5166

South Asian (SAS) AF: 0.603 AC: 2901 AN: 4812

European-Finnish (FIN) AF: 0.715 AC: 7542 AN: 10552

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.644 AC: 43725 AN: 67932

Other (OTH) AF: 0.604 AC: 1275 AN: 2110

Alfa AF: 0.605 Hom.: 11586

Bravo AF: 0.600

Asia WGS AF: 0.572 AC: 1989 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.61
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs2040587; hg19: chr7-114675523;