rs12907752

Variant names:

• chr15-47810997-G-A
• rs12907752
• ENST00000558792.6:n.414+3074C>T

Variant summary

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

The ENST00000558792.6(LINC01491):​n.414+3074C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,202 control chromosomes in the GnomAD database, including 4,320 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 0.20 (4320 hom., cov: 33)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01491	NR_120336.1	n.283-6119C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01491	ENST00000558792.6	n.414+3074C>T		intron_variant	Intron 4 of 6	3
LINC01491	ENST00000651940.1	n.278+3074C>T		intron_variant	Intron 3 of 6
LINC01491	ENST00000653152.1	n.319-6119C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30003 AN: 152084 Hom.: 4307 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0835

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.197 AC: 30046 AN: 152202 Hom.: 4320 Cov.: 33 AF XY: 0.194 AC XY: 14426 AN XY: 74428

African (AFR) AF: 0.403 AC: 16718 AN: 41472

American (AMR) AF: 0.152 AC: 2331 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0835 AC: 290 AN: 3472

East Asian (EAS) AF: 0.145 AC: 751 AN: 5180

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4820

European-Finnish (FIN) AF: 0.0758 AC: 804 AN: 10612

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7570 AN: 68026

Other (OTH) AF: 0.167 AC: 352 AN: 2114

Alfa AF: 0.154 Hom.: 3827

Bravo AF: 0.213

Asia WGS AF: 0.204 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.65
DANN	Benign	0.64
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12907752; hg19: chr15-48103194;