8-93157121-T-C

Position:

• chr8-93157121-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_161372.1(LINC02906):​n.120+9610A>G variant causes a intron, non coding transcript 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 NR_161372.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

Genes affected

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

LOC105375644 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02906	NR_161372.1	n.120+9610A>G		intron_variant, non_coding_transcript_variant
LOC105375644	XR_928417.1	n.60+81T>C		intron_variant, non_coding_transcript_variant
LOC105375644	XR_928416.1	n.60+81T>C		intron_variant, non_coding_transcript_variant
LOC105375644	XR_928419.1	n.60+81T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02906	ENST00000521906.5	n.120+9610A>G		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.314

Alfa AF: 0.298 Hom.: 3615

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs278567; hg19: chr8-94169350;