rs12506479

chr4-73726444-T-C

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 0.273 in 152,164 control chromosomes in the GnomAD database, including 5,949 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 0.27 (5949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41480 AN: 152046 Hom.: 5937 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.273 AC: 41523 AN: 152164 Hom.: 5949 Cov.: 32 AF XY: 0.279 AC XY: 20734 AN XY: 74402

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.265

Alfa AF: 0.272 Hom.: 8364

Bravo AF: 0.279

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.040
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: rs12506479; hg19: chr4-74592161;