chr8-93157121-T-C

Variant names:

• chr8-93157121-T-C
• rs278567
• ENST00000521906.6:n.120+9610A>G

Variant summary

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

The ENST00000521906.6(LINC02906):​n.120+9610A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,986 control chromosomes in the GnomAD database, including 8,188 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 0.32 (8188 hom., cov: 32)
• Consequence: LINC02906 ENST00000521906.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 2 publications found

Genes affected

LINC02906 (HGNC:42974): (long intergenic non-protein coding RNA 2906)

ENSG00000307173 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02906	NR_161372.1	n.120+9610A>G		intron_variant	Intron 1 of 2
LOC105375644	XR_928416.1	n.60+81T>C		intron_variant	Intron 1 of 4
LOC105375644	XR_928417.1	n.60+81T>C		intron_variant	Intron 1 of 4
LOC105375644	XR_928419.1	n.60+81T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02906	ENST00000521906.6	n.120+9610A>G		intron_variant	Intron 1 of 2	1
LINC02906	ENST00000824293.1	n.96+9610A>G		intron_variant	Intron 1 of 2
LINC02906	ENST00000824294.1	n.96+9610A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48959 AN: 151868 Hom.: 8162 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.323 AC: 49027 AN: 151986 Hom.: 8188 Cov.: 32 AF XY: 0.325 AC XY: 24126 AN XY: 74296

African (AFR) AF: 0.403 AC: 16695 AN: 41440

American (AMR) AF: 0.278 AC: 4240 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3464

East Asian (EAS) AF: 0.420 AC: 2158 AN: 5144

South Asian (SAS) AF: 0.376 AC: 1810 AN: 4808

European-Finnish (FIN) AF: 0.295 AC: 3114 AN: 10562

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19358 AN: 67980

Other (OTH) AF: 0.314 AC: 662 AN: 2110

Alfa AF: 0.314 Hom.: 7596

Bravo AF: 0.324

Asia WGS AF: 0.433 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.68
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: rs278567; hg19: chr8-94169350;