2-46795404-A-C

Position:

• chr2-46795404-A-C

Variant summary

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

The ENST00000650611.1(LINC01118):​n.173-1915A>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 0.0709 in 152,098 control chromosomes in the GnomAD database, including 565 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 0.071 (565 hom., cov: 32)
• Consequence: LINC01118 ENST00000650611.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

Genes affected

LINC01118 (HGNC:49261): (long intergenic non-protein coding RNA 1118)

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 (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01118	ENST00000650611.1	n.173-1915A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0709 AC: 10773 AN: 151980 Hom.: 564 Cov.: 32

Gnomad AFR AF: 0.0960

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0669

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.0905

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0463

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0709 AC: 10779 AN: 152098 Hom.: 565 Cov.: 32 AF XY: 0.0717 AC XY: 5331 AN XY: 74358

Gnomad4 AFR AF: 0.0962

Gnomad4 AMR AF: 0.0476

Gnomad4 ASJ AF: 0.0669

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.0906

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.0463

Gnomad4 OTH AF: 0.0664

Alfa AF: 0.0626 Hom.: 555

Bravo AF: 0.0716

Asia WGS AF: 0.155 AC: 537 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	0.14
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs76351433; hg19: chr2-47022543;