2-41888764-T-G

Position:

• chr2-41888764-T-G

Variant summary

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

The NR_033996.1(LINC01913):​n.225-1587T>G 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 0.665 in 151,874 control chromosomes in the GnomAD database, including 33,720 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 0.67 (33720 hom., cov: 31)
• Consequence: LINC01913 NR_033996.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

Genes affected

LINC01913 (HGNC:52732): (long intergenic non-protein coding RNA 1913)

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 (SAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01913	NR_033996.1	n.225-1587T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01913	ENST00000653206.1	n.303-1587T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100945 AN: 151756 Hom.: 33682 Cov.: 31

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.665 AC: 101038 AN: 151874 Hom.: 33720 Cov.: 31 AF XY: 0.669 AC XY: 49658 AN XY: 74216

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.664

Alfa AF: 0.622 Hom.: 3186

Bravo AF: 0.659

Asia WGS AF: 0.738 AC: 2565 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	2.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4358170; hg19: chr2-42115904;