rs10490098

Positions:

• chr2-58902806-G-A

Variant summary

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

The ENST00000427421.5(LINC01122):​n.425-9913G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,172 control chromosomes in the GnomAD database, including 1,696 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 0.13 (1696 hom., cov: 32)
• Consequence: LINC01122 ENST00000427421.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

Genes affected

LINC01122 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.425-9913G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.5	n.503-21739G>A		intron_variant		3
LINC01122	ENST00000422793.3	n.361-21739G>A		intron_variant		5
LINC01122	ENST00000427421.5	n.425-9913G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19928 AN: 152054 Hom.: 1700 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.131 AC: 19915 AN: 152172 Hom.: 1696 Cov.: 32 AF XY: 0.138 AC XY: 10285 AN XY: 74384

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.122

Alfa AF: 0.112 Hom.: 1094

Bravo AF: 0.133

Asia WGS AF: 0.260 AC: 901 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490098; hg19: chr2-59129941;