rs6743916

chr2-58477314-G-Achr2-58477314-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000452840.5(LINC01122):n.195+15469G>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 0.356 in 151,992 control chromosomes in the GnomAD database, including 10,208 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 0.36 (10208 hom., cov: 33)
• Consequence: LINC01122 ENST00000452840.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01122	ENST00000452840.5	n.195+15469G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000686174.2	n.157+2220C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54093 AN: 151874 Hom.: 10191 Cov.: 33

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.356 AC: 54144 AN: 151992 Hom.: 10208 Cov.: 33 AF XY: 0.355 AC XY: 26403 AN XY: 74288

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.370

Alfa AF: 0.305 Hom.: 14731

Bravo AF: 0.367

Asia WGS AF: 0.457 AC: 1587 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	9.8
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6743916; hg19: chr2-58704449;