rs17432750

Variant names:

• chr5-56735995-C-A
• rs17432750

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.131 in 152,188 control chromosomes in the GnomAD database, including 1,520 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 0.13 (1520 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.162 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: 0.131 AC: 19895 AN: 152070 Hom.: 1520 Cov.: 32

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0440

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.131 AC: 19900 AN: 152188 Hom.: 1520 Cov.: 32 AF XY: 0.132 AC XY: 9842 AN XY: 74394

African (AFR) AF: 0.0721 AC: 2995 AN: 41556

American (AMR) AF: 0.164 AC: 2500 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3470

East Asian (EAS) AF: 0.0441 AC: 228 AN: 5174

South Asian (SAS) AF: 0.172 AC: 827 AN: 4822

European-Finnish (FIN) AF: 0.171 AC: 1806 AN: 10568

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10794 AN: 67990

Other (OTH) AF: 0.126 AC: 267 AN: 2116

Alfa AF: 0.153 Hom.: 1065

Bravo AF: 0.127

Asia WGS AF: 0.0890 AC: 309 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	19
DANN	Benign	0.79
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs17432750; hg19: chr5-56031822;