4-12669937-C-T

Position:

• chr4-12669937-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 0.292 in 151,932 control chromosomes in the GnomAD database, including 7,418 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 0.29 (7418 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12669937C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44395 AN: 151814 Hom.: 7408 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.292 AC: 44407 AN: 151932 Hom.: 7418 Cov.: 32 AF XY: 0.303 AC XY: 22490 AN XY: 74238

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.287

Alfa AF: 0.300 Hom.: 3933

Bravo AF: 0.289

Asia WGS AF: 0.557 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516259; hg19: chr4-12671561;