rs12654032

Variant names:

• chr5-136098920-A-G
• rs12654032

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0178 AC: 740 AN: 41578

American (AMR) AF: 0.0827 AC: 1266 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1264 AN: 5182

South Asian (SAS) AF: 0.0696 AC: 336 AN: 4828

European-Finnish (FIN) AF: 0.0577 AC: 613 AN: 10616

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0722 AC: 4914 AN: 68028

Other (OTH) AF: 0.0829 AC: 175 AN: 2110

Alfa AF: 0.0720 Hom.: 692

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12654032; hg19: chr5-135434609;