6-158878184-T-C

Variant names:

• chr6-158878184-T-C
• rs9457490
• ENST00000367072.6:n.164+8207T>C

Variant summary

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

The ENST00000367072.6(LINC02901):​n.164+8207T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,188 control chromosomes in the GnomAD database, including 48,007 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 0.78 (48007 hom., cov: 33)
• Consequence: LINC02901 ENST00000367072.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 5 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02901	NR_160976.1	n.282+7874T>C		intron_variant	Intron 1 of 2
LINC02901	NR_160977.1	n.258+4563T>C		intron_variant	Intron 2 of 3
LINC02901	NR_160978.1	n.152+8219T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02901	ENST00000367072.6	n.164+8207T>C		intron_variant	Intron 1 of 2	5
LINC02901	ENST00000367073.9	n.591+4563T>C		intron_variant	Intron 2 of 3	5
LINC02901	ENST00000486232.3	n.150+8219T>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118707 AN: 152070 Hom.: 47944 Cov.: 33

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.781 AC: 118820 AN: 152188 Hom.: 48007 Cov.: 33 AF XY: 0.775 AC XY: 57692 AN XY: 74394

African (AFR) AF: 0.928 AC: 38540 AN: 41548

American (AMR) AF: 0.549 AC: 8378 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2520 AN: 3466

East Asian (EAS) AF: 0.293 AC: 1516 AN: 5176

South Asian (SAS) AF: 0.720 AC: 3476 AN: 4828

European-Finnish (FIN) AF: 0.840 AC: 8895 AN: 10592

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52938 AN: 68000

Other (OTH) AF: 0.737 AC: 1556 AN: 2112

Alfa AF: 0.760 Hom.: 202593

Bravo AF: 0.761

Asia WGS AF: 0.538 AC: 1869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.6
DANN	Benign	0.75
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs9457490; hg19: chr6-159299216;