10-120748813-T-G

Variant names:

• chr10-120748813-T-G
• rs3011415
• ENST00000655330.1:n.341-75573T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000655330.1(LINC02930):​n.341-75573T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,192 control chromosomes in the GnomAD database, including 48,533 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 0.80 (48533 hom., cov: 33)
• Consequence: LINC02930 ENST00000655330.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 2 publications found

Genes affected

LINC02930 (HGNC:55821): (long intergenic non-protein coding RNA 2930)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02930	XR_002957103.2	n.401-63218T>G		intron_variant	Intron 2 of 4
LINC02930	XR_007062314.1	n.1111-63218T>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02930	ENST00000655330.1	n.341-75573T>G		intron_variant	Intron 2 of 3
LINC02930	ENST00000659883.1	n.403-63218T>G		intron_variant	Intron 2 of 6
LINC02930	ENST00000663713.2	n.403-63218T>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121358 AN: 152072 Hom.: 48509 Cov.: 33

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.798 AC: 121434 AN: 152192 Hom.: 48533 Cov.: 33 AF XY: 0.795 AC XY: 59119 AN XY: 74392

African (AFR) AF: 0.794 AC: 32970 AN: 41516

American (AMR) AF: 0.765 AC: 11687 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2617 AN: 3468

East Asian (EAS) AF: 0.648 AC: 3355 AN: 5174

South Asian (SAS) AF: 0.725 AC: 3497 AN: 4822

European-Finnish (FIN) AF: 0.818 AC: 8675 AN: 10600

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 56035 AN: 68014

Other (OTH) AF: 0.779 AC: 1646 AN: 2112

Alfa AF: 0.814 Hom.: 100463

Bravo AF: 0.795

Asia WGS AF: 0.710 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	18
DANN	Benign	0.78
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs3011415; hg19: chr10-122508325;