10-120624292-A-G

Position:

• chr10-120624292-A-G

Variant summary

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

The ENST00000655330.1(LINC02930):​n.133-11650A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,944 control chromosomes in the GnomAD database, including 13,017 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 0.41 (13017 hom., cov: 32)
• Consequence: LINC02930 ENST00000655330.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

LINC02930 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02930	XR_002957103.2	n.193-11650A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02930	ENST00000655330.1	n.133-11650A>G		intron_variant
LINC02930	ENST00000659883.1	n.195-11650A>G		intron_variant
LINC02930	ENST00000663713.1	n.193-11650A>G		intron_variant
LINC02930	ENST00000665554.1	n.178-11650A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61928 AN: 151828 Hom.: 13019 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.408 AC: 61941 AN: 151944 Hom.: 13017 Cov.: 32 AF XY: 0.407 AC XY: 30213 AN XY: 74262

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.416

Alfa AF: 0.427 Hom.: 28442

Bravo AF: 0.409

Asia WGS AF: 0.484 AC: 1682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2901256; hg19: chr10-122383804;