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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02930	XR_002957103.2	n.400+34108T>C		intron_variant	Intron 2 of 4
LINC02930	XR_007062314.1	n.1110+34108T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02930	ENST00000655330.1	n.340+34108T>C		intron_variant	Intron 2 of 3
LINC02930	ENST00000659883.1	n.402+34108T>C		intron_variant	Intron 2 of 6
LINC02930	ENST00000663713.2	n.402+34108T>C		intron_variant	Intron 2 of 4

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 v4.3

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;