rs12654032

chr5-136098920-A-G

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 0.0627 in 152,322 control chromosomes in the GnomAD database, including 473 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 0.063 (473 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 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: 0.0627 AC: 9543 AN: 152204 Hom.: 471 Cov.: 33

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0830

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.0702

Gnomad FIN AF: 0.0577

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0723

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0627 AC: 9543 AN: 152322 Hom.: 473 Cov.: 33 AF XY: 0.0645 AC XY: 4804 AN XY: 74490

Gnomad4 AFR AF: 0.0178

Gnomad4 AMR AF: 0.0827

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.0696

Gnomad4 FIN AF: 0.0577

Gnomad4 NFE AF: 0.0722

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0732 Hom.: 542

Bravo AF: 0.0650

Asia WGS AF: 0.168 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.79
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12654032; hg19: chr5-135434609;