rs16960139

Variant names:

• chr15-47792483-G-A
• rs16960139
• ENST00000558792.6:n.571+10901C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558792.6(LINC01491):​n.571+10901C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0273 in 152,286 control chromosomes in the GnomAD database, including 229 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 0.027 (229 hom., cov: 33)
• Consequence: LINC01491 ENST00000558792.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 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+10901C>T		intron_variant	Intron 6 of 6	3
LINC01491	ENST00000651940.1	n.436-1233C>T		intron_variant	Intron 5 of 6
LINC01491	ENST00000653152.1	n.476-1233C>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.0273 AC: 4150 AN: 152168 Hom.: 231 Cov.: 33

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00700

Gnomad OTH AF: 0.0312

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

GnomAD4 genome AF: 0.0273 AC: 4155 AN: 152286 Hom.: 229 Cov.: 33 AF XY: 0.0287 AC XY: 2139 AN XY: 74480

Gnomad4 AFR AF: 0.0313

Gnomad4 AMR AF: 0.0619

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.0336

Gnomad4 FIN AF: 0.00339

Gnomad4 NFE AF: 0.00698

Gnomad4 OTH AF: 0.0313

Alfa AF: 0.0117 Hom.: 9

Bravo AF: 0.0331

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.068
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960139; hg19: chr15-48084680;