rs596942

Variant names:

• chr15-47789954-C-T
• rs596942
• ENST00000558792.6:n.571+13430G>A

Variant summary

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

The ENST00000558792.6(LINC01491):​n.571+13430G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 152,126 control chromosomes in the GnomAD database, including 965 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 0.090 (965 hom., cov: 33)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 2 publications found

Genes affected

LINC01491 (HGNC:51148): (long intergenic non-protein coding RNA 1491)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 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
LINC01491	ENST00000558792.6	n.571+13430G>A		intron_variant	Intron 6 of 6	3
LINC01491	ENST00000651940.1	n.579+1153G>A		intron_variant	Intron 6 of 6
LINC01491	ENST00000653152.1	n.619+1153G>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.0901 AC: 13699 AN: 152008 Hom.: 965 Cov.: 33

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0575

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.0901 AC: 13712 AN: 152126 Hom.: 965 Cov.: 33 AF XY: 0.0955 AC XY: 7101 AN XY: 74366

African (AFR) AF: 0.0844 AC: 3505 AN: 41520

American (AMR) AF: 0.140 AC: 2143 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0447 AC: 155 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2232 AN: 5154

South Asian (SAS) AF: 0.0788 AC: 380 AN: 4820

European-Finnish (FIN) AF: 0.103 AC: 1089 AN: 10576

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0574 AC: 3906 AN: 67998

Other (OTH) AF: 0.0881 AC: 186 AN: 2112

Alfa AF: 0.0768 Hom.: 519

Bravo AF: 0.0987

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.62
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs596942; hg19: chr15-48082151;