chr6-158919640-A-C

Variant names:

• chr6-158919640-A-C
• rs9365009
• ENST00000795721.1:n.275+24274A>C

Variant summary

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

The ENST00000795721.1(LINC02901):​n.275+24274A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,972 control chromosomes in the GnomAD database, including 12,214 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 0.37 (12214 hom., cov: 32)
• Consequence: LINC02901 ENST00000795721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 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.275+24274A>C		intron_variant	Intron 2 of 2
LINC02901	ENST00000795722.1	n.502-28406A>C		intron_variant	Intron 2 of 2
LINC02901	ENST00000795723.1	n.429-9539A>C		intron_variant	Intron 2 of 2
LINC02901	ENST00000795724.1	n.315-9539A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56489 AN: 151854 Hom.: 12168 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.372 AC: 56593 AN: 151972 Hom.: 12214 Cov.: 32 AF XY: 0.378 AC XY: 28091 AN XY: 74264

African (AFR) AF: 0.487 AC: 20199 AN: 41436

American (AMR) AF: 0.504 AC: 7689 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3468

East Asian (EAS) AF: 0.809 AC: 4180 AN: 5170

South Asian (SAS) AF: 0.497 AC: 2395 AN: 4820

European-Finnish (FIN) AF: 0.269 AC: 2836 AN: 10544

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 17004 AN: 67958

Other (OTH) AF: 0.387 AC: 812 AN: 2100

Alfa AF: 0.303 Hom.: 24111

Bravo AF: 0.401

Asia WGS AF: 0.629 AC: 2186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.73
DANN	Benign	0.69
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs9365009; hg19: chr6-159340672;