5-121633621-C-A

Position:

• chr5-121633621-C-A

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 0.849 in 151,926 control chromosomes in the GnomAD database, including 54,913 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 0.85 (54913 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 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: 0.850 AC: 128970 AN: 151808 Hom.: 54883 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.849 AC: 129053 AN: 151926 Hom.: 54913 Cov.: 31 AF XY: 0.846 AC XY: 62834 AN XY: 74234

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.859

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.846

Alfa AF: 0.846 Hom.: 97884

Bravo AF: 0.859

Asia WGS AF: 0.790 AC: 2747 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9327207; hg19: chr5-120969316;