chr2-58974894-G-C

Position:

• chr2-58974894-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_033873.1(LINC01122):​n.834-29055G>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 0.0257 in 149,100 control chromosomes in the GnomAD database, including 69 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 0.026 (69 hom., cov: 32)
• Consequence: LINC01122 NR_033873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

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=-0.72).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0257 (3826/149100) while in subpopulation NFE AF= 0.0371 (2506/67534). AF 95% confidence interval is 0.0359. There are 69 homozygotes in gnomad4. There are 1768 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 69 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01122	NR_033873.1	n.834-29055G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01122	ENST00000452840.5	n.816-29055G>C		intron_variant, non_coding_transcript_variant		5
LINC01122	ENST00000427421.5	n.834-29055G>C		intron_variant, non_coding_transcript_variant		2
LINC01122	ENST00000449448.6	n.639-29055G>C		intron_variant, non_coding_transcript_variant		3
LINC01122	ENST00000650056.1	n.674-29055G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0257 AC: 3829 AN: 149006 Hom.: 70 Cov.: 32

Gnomad AFR AF: 0.00738

Gnomad AMI AF: 0.0210

Gnomad AMR AF: 0.0260

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00781

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0260

Gnomad NFE AF: 0.0371

Gnomad OTH AF: 0.0277

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

GnomAD4 genome AF: 0.0257 AC: 3826 AN: 149100 Hom.: 69 Cov.: 32 AF XY: 0.0244 AC XY: 1768 AN XY: 72446

Gnomad4 AFR AF: 0.00736

Gnomad4 AMR AF: 0.0259

Gnomad4 ASJ AF: 0.0934

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00784

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0371

Gnomad4 OTH AF: 0.0269

Alfa AF: 0.0274 Hom.: 8

Bravo AF: 0.0262

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	14
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs111835151; hg19: chr2-59202029;