rs17470528

chr4-48049986-T-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 0.129 in 152,236 control chromosomes in the GnomAD database, including 1,633 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 (1633 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.251 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: 0.129 AC: 19612 AN: 152118 Hom.: 1633 Cov.: 32

Gnomad AFR AF: 0.0332

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.129 AC: 19612 AN: 152236 Hom.: 1633 Cov.: 32 AF XY: 0.131 AC XY: 9750 AN XY: 74444

Gnomad4 AFR AF: 0.0331

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.126

Alfa AF: 0.174 Hom.: 4902

Bravo AF: 0.118

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.94
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17470528; hg19: chr4-48052003;