rs17470528

Variant names:

• chr4-48049986-T-C
• rs17470528

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 0.129 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
• Publications: 9 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0331 AC: 1374 AN: 41548

American (AMR) AF: 0.107 AC: 1639 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3472

East Asian (EAS) AF: 0.111 AC: 575 AN: 5190

South Asian (SAS) AF: 0.263 AC: 1269 AN: 4824

European-Finnish (FIN) AF: 0.134 AC: 1418 AN: 10588

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12228 AN: 68014

Other (OTH) AF: 0.126 AC: 266 AN: 2112

Alfa AF: 0.163 Hom.: 7137

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
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs17470528; hg19: chr4-48052003;