rs76351433

Variant names:

• chr2-46795404-A-C
• rs76351433
• ENST00000650611.1:n.173-1915A>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01118	ENST00000650611.1	n.173-1915A>C		intron_variant	Intron 1 of 7

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;