chr4-12669937-C-T

Variant names:

• chr4-12669937-C-T
• rs10516259

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;