rs12436436

Variant names:

• chr14-23912306-T-C
• rs12436436
• XR_001750659.1:n.196-9594A>G

Variant summary

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

The XR_001750659.1(LINC00596):​n.196-9594A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,110 control chromosomes in the GnomAD database, including 1,999 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 0.14 (1999 hom., cov: 32)
• Consequence: LINC00596 XR_001750659.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 13 publications found

Genes affected

LINC00596 (HGNC:23167): (long intergenic non-protein coding RNA 596) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21449 AN: 151992 Hom.: 1988 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0716

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0596

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0891

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.141 AC: 21483 AN: 152110 Hom.: 1999 Cov.: 32 AF XY: 0.141 AC XY: 10462 AN XY: 74372

African (AFR) AF: 0.261 AC: 10819 AN: 41440

American (AMR) AF: 0.118 AC: 1804 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0716 AC: 248 AN: 3464

East Asian (EAS) AF: 0.188 AC: 968 AN: 5156

South Asian (SAS) AF: 0.113 AC: 544 AN: 4818

European-Finnish (FIN) AF: 0.0596 AC: 632 AN: 10606

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0891 AC: 6057 AN: 68014

Other (OTH) AF: 0.135 AC: 286 AN: 2116

Alfa AF: 0.0973 Hom.: 2188

Bravo AF: 0.149

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
DANN	Benign	0.48
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs12436436; hg19: chr14-24381515;