chr5-123663126-A-C

Variant names:

• chr5-123663126-A-C
• rs17150546

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0449 AC: 1865 AN: 41562

American (AMR) AF: 0.0978 AC: 1494 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 157 AN: 3470

East Asian (EAS) AF: 0.104 AC: 539 AN: 5186

South Asian (SAS) AF: 0.114 AC: 549 AN: 4822

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10608

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0638 AC: 4337 AN: 68014

Other (OTH) AF: 0.0888 AC: 188 AN: 2116

Alfa AF: 0.0770 Hom.: 175

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
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs17150546; hg19: chr5-122998820;