rs12500918

chr4-152747856-A-Cchr4-152747856-A-Gchr4-152747856-A-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 0.482 in 152,036 control chromosomes in the GnomAD database, including 17,847 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 0.48 (17847 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 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: 0.482 AC: 73203 AN: 151918 Hom.: 17816 Cov.: 33

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.482 AC: 73276 AN: 152036 Hom.: 17847 Cov.: 33 AF XY: 0.488 AC XY: 36257 AN XY: 74326

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.452

Alfa AF: 0.445 Hom.: 33669

Bravo AF: 0.473

Asia WGS AF: 0.551 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	15
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12500918; hg19: chr4-153669008;