6-158947492-G-T

Variant names:

• chr6-158947492-G-T
• rs12216499
• ENST00000795721.1:n.276-554G>T

Variant summary

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

The ENST00000795721.1(LINC02901):​n.276-554G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,226 control chromosomes in the GnomAD database, including 1,715 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 0.11 (1715 hom., cov: 32)
• Consequence: LINC02901 ENST00000795721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 22 publications found

Genes affected

LINC02901 (HGNC:21179): (long intergenic non-protein coding RNA 2901)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.398 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
LINC02901	ENST00000795721.1	n.276-554G>T		intron_variant	Intron 2 of 2
LINC02901	ENST00000795722.1	n.502-554G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17323 AN: 152106 Hom.: 1704 Cov.: 32

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0758

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.114 AC: 17370 AN: 152226 Hom.: 1715 Cov.: 32 AF XY: 0.120 AC XY: 8911 AN XY: 74430

African (AFR) AF: 0.0757 AC: 3144 AN: 41548

American (AMR) AF: 0.282 AC: 4310 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2136 AN: 5172

South Asian (SAS) AF: 0.194 AC: 936 AN: 4826

European-Finnish (FIN) AF: 0.0906 AC: 961 AN: 10606

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0758 AC: 5156 AN: 68014

Other (OTH) AF: 0.130 AC: 275 AN: 2114

Alfa AF: 0.102 Hom.: 802

Bravo AF: 0.133

Asia WGS AF: 0.282 AC: 981 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	0.48
DANN	Benign	0.55
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs12216499; hg19: chr6-159368524;