rs9457532

Variant names:

• chr6-158931837-C-A
• rs9457532
• ENST00000795721.1:n.276-16209C>A

Variant summary

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

The ENST00000795721.1(LINC02901):​n.276-16209C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0315 in 151,104 control chromosomes in the GnomAD database, including 144 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 0.031 (144 hom., cov: 32)
• Consequence: LINC02901 ENST00000795721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0512 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.276-16209C>A		intron_variant	Intron 2 of 2
LINC02901	ENST00000795722.1	n.502-16209C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0315 AC: 4750 AN: 150986 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0295

Gnomad ASJ AF: 0.00950

Gnomad EAS AF: 0.000215

Gnomad SAS AF: 0.0107

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0251

Gnomad OTH AF: 0.0245

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

GnomAD4 genome AF: 0.0315 AC: 4758 AN: 151104 Hom.: 144 Cov.: 32 AF XY: 0.0301 AC XY: 2218 AN XY: 73720

African (AFR) AF: 0.0531 AC: 2203 AN: 41494

American (AMR) AF: 0.0295 AC: 449 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.00950 AC: 33 AN: 3472

East Asian (EAS) AF: 0.000215 AC: 1 AN: 4654

South Asian (SAS) AF: 0.0107 AC: 49 AN: 4580

European-Finnish (FIN) AF: 0.0162 AC: 169 AN: 10410

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0252 AC: 1710 AN: 67962

Other (OTH) AF: 0.0243 AC: 51 AN: 2100

Alfa AF: 0.0351 Hom.: 32

Bravo AF: 0.0329

Asia WGS AF: 0.0140 AC: 46 AN: 3276

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.74
DANN	Benign	0.50
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs9457532; hg19: chr6-159352869;