chr5-5609582-C-A

Variant names:

• chr5-5609582-C-A
• rs378932

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 0.702 in 152,072 control chromosomes in the GnomAD database, including 37,776 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 0.70 (37776 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.13).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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: 0.702 AC: 106663 AN: 151954 Hom.: 37749 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.702 AC: 106737 AN: 152072 Hom.: 37776 Cov.: 32 AF XY: 0.709 AC XY: 52720 AN XY: 74314

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.681

Alfa AF: 0.694 Hom.: 33775

Bravo AF: 0.701

Asia WGS AF: 0.845 AC: 2942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0030
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs378932; hg19: chr5-5609695;