rs12436436

Positions:

• chr14-23912306-T-C

Variant summary

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

The XR_001750659.1(LINC00596):​n.196-9594A>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 0.141 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

Genes affected

LINC00596 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00596	XR_001750659.1	n.196-9594A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0716

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0596

Gnomad4 NFE AF: 0.0891

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0950 Hom.: 1201

Bravo AF: 0.149

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12436436; hg19: chr14-24381515;