2-58838673-G-A

Position:

• chr2-58838673-G-A

Variant summary

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

The NR_033873.1(LINC01122):​n.248-11757G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,890 control chromosomes in the GnomAD database, including 1,652 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 0.14 (1652 hom., cov: 32)
• Consequence: LINC01122 NR_033873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352

Genes affected

LINC01122 (HGNC:49267): (long intergenic non-protein coding RNA 1122)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01122	NR_033873.1	n.248-11757G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01122	ENST00000452840.5	n.258-11757G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21332 AN: 151772 Hom.: 1649 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.141 AC: 21351 AN: 151890 Hom.: 1652 Cov.: 32 AF XY: 0.141 AC XY: 10446 AN XY: 74256

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0921

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.145

Alfa AF: 0.120 Hom.: 2395

Bravo AF: 0.145

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.57
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7593324; hg19: chr2-59065808;