rs4408389

Positions:

• chr12-24696707-C-T

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 0.408 in 152,048 control chromosomes in the GnomAD database, including 13,482 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 0.41 (13482 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.24696707C>T		intergenic_region
LOC105369698	XR_001749046.2	n.326+8639G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61937 AN: 151930 Hom.: 13474 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.408 AC: 61969 AN: 152048 Hom.: 13482 Cov.: 32 AF XY: 0.407 AC XY: 30286 AN XY: 74322

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.0957

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.377

Alfa AF: 0.471 Hom.: 12735

Bravo AF: 0.385

Asia WGS AF: 0.244 AC: 849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4408389; hg19: chr12-24849641;