chr2-45233954-C-T

Position:

• chr2-45233954-C-T

Variant summary

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

The NR_033831.1(LINC01121):​n.275+20713G>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 0.867 in 152,228 control chromosomes in the GnomAD database, including 57,461 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 0.87 (57461 hom., cov: 33)
• Consequence: LINC01121 NR_033831.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

Genes affected

LINC01121 (HGNC:49266): (long intergenic non-protein coding RNA 1121)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01121	NR_033831.1	n.275+20713G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01121	ENST00000378479.5	n.275+20713G>A		intron_variant, non_coding_transcript_variant		1
LINC01121	ENST00000658738.1	n.709-41669G>A		intron_variant, non_coding_transcript_variant
LINC01121	ENST00000427020.6	n.705-22294G>A		intron_variant, non_coding_transcript_variant		3
LINC01121	ENST00000430650.2	n.717-41669G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131897 AN: 152110 Hom.: 57421 Cov.: 33

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.867 AC: 131993 AN: 152228 Hom.: 57461 Cov.: 33 AF XY: 0.865 AC XY: 64365 AN XY: 74424

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.870

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.853

Alfa AF: 0.847 Hom.: 6824

Bravo AF: 0.876

Asia WGS AF: 0.858 AC: 2984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2194398; hg19: chr2-45461093;