5-32604515-G-C

Position:

• chr5-32604515-G-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 0.268 in 151,964 control chromosomes in the GnomAD database, including 6,804 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 0.27 (6804 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40697 AN: 151846 Hom.: 6800 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.268 AC: 40693 AN: 151964 Hom.: 6804 Cov.: 32 AF XY: 0.269 AC XY: 19997 AN XY: 74258

Gnomad4 AFR AF: 0.0746

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.273

Alfa AF: 0.303 Hom.: 958

Bravo AF: 0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.41
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11744644; hg19: chr5-32604621;