rs76351433

Variant names:

• chr2-46795404-A-C
• rs76351433
• ENST00000650611.2:n.173-1915A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650611.2(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 ENST00000650611.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650611.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01118	ENST00000650611.2		n.173-1915A>C		intron	N/A

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

African (AFR) AF: 0.0962 AC: 3993 AN: 41496

American (AMR) AF: 0.0476 AC: 727 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0669 AC: 232 AN: 3470

East Asian (EAS) AF: 0.283 AC: 1460 AN: 5164

South Asian (SAS) AF: 0.0906 AC: 437 AN: 4824

European-Finnish (FIN) AF: 0.0592 AC: 627 AN: 10586

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0463 AC: 3146 AN: 67972

Other (OTH) AF: 0.0664 AC: 140 AN: 2110

Alfa AF: 0.0625 Hom.: 776

Bravo AF: 0.0716

Asia WGS AF: 0.155 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.36
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs76351433; hg19: chr2-47022543;