rs6719884

Positions:

• chr2-58809781-A-C
• chr2-58809781-A-G

Variant summary

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

The NR_033873.1(LINC01122):​n.248-40649A>C 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 0.563 in 151,920 control chromosomes in the GnomAD database, including 24,135 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 0.56 (24135 hom., cov: 32)
• Consequence: LINC01122 NR_033873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.248-40649A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000452840.5	n.258-40649A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85427 AN: 151802 Hom.: 24114 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.563 AC: 85488 AN: 151920 Hom.: 24135 Cov.: 32 AF XY: 0.561 AC XY: 41622 AN XY: 74232

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.576

Alfa AF: 0.578 Hom.: 18057

Bravo AF: 0.565

Asia WGS AF: 0.615 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6719884; hg19: chr2-59036916;