12-113604401-A-G

Position:

• chr12-113604401-A-G

Variant summary

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

The variant allele was found at a frequency of 0.348 in 151,950 control chromosomes in the GnomAD database, including 9,561 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 0.35 (9561 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.113604401A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01234	ENST00000661760.1	n.313-18769T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52775 AN: 151832 Hom.: 9557 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.348 AC: 52831 AN: 151950 Hom.: 9561 Cov.: 31 AF XY: 0.345 AC XY: 25659 AN XY: 74270

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.334

Alfa AF: 0.318 Hom.: 1699

Bravo AF: 0.354

Asia WGS AF: 0.347 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4766691; hg19: chr12-114042206;