17-58283476-C-T

Variant names:

• chr17-58283476-C-T
• rs4401102

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 0.271 in 152,064 control chromosomes in the GnomAD database, including 6,032 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 0.27 (6032 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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: 0.271 AC: 41116 AN: 151946 Hom.: 6020 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.271 AC: 41166 AN: 152064 Hom.: 6032 Cov.: 32 AF XY: 0.269 AC XY: 19958 AN XY: 74322

African (AFR) AF: 0.377 AC: 15640 AN: 41438

American (AMR) AF: 0.234 AC: 3580 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1086 AN: 3470

East Asian (EAS) AF: 0.122 AC: 631 AN: 5186

South Asian (SAS) AF: 0.173 AC: 832 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2396 AN: 10576

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.237 AC: 16116 AN: 67986

Other (OTH) AF: 0.287 AC: 605 AN: 2108

Alfa AF: 0.224 Hom.: 2345

Bravo AF: 0.278

Asia WGS AF: 0.143 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.44
DANN	Benign	0.33
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4401102; hg19: chr17-56360837;