rs17536530

Variant names:

• chr4-46131706-A-C
• rs17536530

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 0.0531 in 152,106 control chromosomes in the GnomAD database, including 310 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 0.053 (310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.077 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: 0.0531 AC: 8078 AN: 151988 Hom.: 310 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.0975

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0701

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0531 AC: 8070 AN: 152106 Hom.: 310 Cov.: 32 AF XY: 0.0553 AC XY: 4112 AN XY: 74350

African (AFR) AF: 0.0125 AC: 519 AN: 41532

American (AMR) AF: 0.0342 AC: 522 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0975 AC: 338 AN: 3466

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5168

South Asian (SAS) AF: 0.0837 AC: 404 AN: 4828

European-Finnish (FIN) AF: 0.116 AC: 1227 AN: 10586

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

European-Non Finnish (NFE) AF: 0.0701 AC: 4761 AN: 67954

Other (OTH) AF: 0.0459 AC: 97 AN: 2112

Alfa AF: 0.0523 Hom.: 250

Bravo AF: 0.0448

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	16
DANN	Benign	0.68
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs17536530; hg19: chr4-46133723;