chr5-136098920-A-G

Variant names:

• chr5-136098920-A-G
• rs12654032

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 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

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;