rs12652860

chr5-1453657-A-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 0.689 in 152,164 control chromosomes in the GnomAD database, including 36,351 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 0.69 (36351 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.781 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: 0.689 AC: 104739 AN: 152046 Hom.: 36340 Cov.: 33

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.689 AC: 104784 AN: 152164 Hom.: 36351 Cov.: 33 AF XY: 0.693 AC XY: 51550 AN XY: 74408

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.709

Alfa AF: 0.710 Hom.: 7806

Bravo AF: 0.680

Asia WGS AF: 0.699 AC: 2433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.1
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12652860; hg19: chr5-1453772;