10-120670257-T-C

Variant names:

• chr10-120670257-T-C
• rs7475474
• ENST00000655330.1:n.340+34108T>C

Variant summary

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

The ENST00000655330.1(LINC02930):​n.340+34108T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,902 control chromosomes in the GnomAD database, including 11,658 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 0.39 (11658 hom., cov: 31)
• Consequence: LINC02930 ENST00000655330.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655330.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02930	ENST00000655330.1		n.340+34108T>C		intron	N/A
	LINC02930	ENST00000659883.1		n.402+34108T>C		intron	N/A
	LINC02930	ENST00000663713.2		n.402+34108T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58927 AN: 151784 Hom.: 11654 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.388 AC: 58956 AN: 151902 Hom.: 11658 Cov.: 31 AF XY: 0.389 AC XY: 28887 AN XY: 74228

African (AFR) AF: 0.309 AC: 12806 AN: 41406

American (AMR) AF: 0.458 AC: 6977 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2526 AN: 5148

South Asian (SAS) AF: 0.455 AC: 2188 AN: 4812

European-Finnish (FIN) AF: 0.369 AC: 3894 AN: 10548

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27969 AN: 67958

Other (OTH) AF: 0.391 AC: 825 AN: 2108

Alfa AF: 0.404 Hom.: 4874

Bravo AF: 0.391

Asia WGS AF: 0.447 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.36
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs7475474; hg19: chr10-122429769;