5-123663126-A-C

Position:

• chr5-123663126-A-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 0.068 in 152,256 control chromosomes in the GnomAD database, including 429 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 0.068 (429 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.106 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: 0.0679 AC: 10329 AN: 152138 Hom.: 421 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.0883

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

GnomAD4 genome AF: 0.0680 AC: 10351 AN: 152256 Hom.: 429 Cov.: 32 AF XY: 0.0712 AC XY: 5303 AN XY: 74444

Gnomad4 AFR AF: 0.0449

Gnomad4 AMR AF: 0.0978

Gnomad4 ASJ AF: 0.0452

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0638

Gnomad4 OTH AF: 0.0888

Alfa AF: 0.0788 Hom.: 74

Bravo AF: 0.0675

Asia WGS AF: 0.147 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17150546; hg19: chr5-122998820;