chr2-58820784-T-G

Position:

• chr2-58820784-T-G

Variant summary

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

The ENST00000427421.5(LINC01122):​n.248-29646T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,090 control chromosomes in the GnomAD database, including 41,656 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 0.74 (41656 hom., cov: 32)
• Consequence: LINC01122 ENST00000427421.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262

Genes affected

LINC01122 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.248-29646T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.5	n.326-29646T>G		intron_variant		3
LINC01122	ENST00000422793.3	n.184-29646T>G		intron_variant		5
LINC01122	ENST00000427421.5	n.248-29646T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112143 AN: 151972 Hom.: 41610 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.738 AC: 112243 AN: 152090 Hom.: 41656 Cov.: 32 AF XY: 0.740 AC XY: 55008 AN XY: 74336

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.721

Alfa AF: 0.699 Hom.: 75149

Bravo AF: 0.736

Asia WGS AF: 0.726 AC: 2524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2160206; hg19: chr2-59047919;