rs17608635

Variant names:

• chr4-45077659-G-A
• rs17608635

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 0.226 in 151,930 control chromosomes in the GnomAD database, including 4,030 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 0.23 (4030 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34315 AN: 151812 Hom.: 4027 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.226 AC: 34332 AN: 151930 Hom.: 4030 Cov.: 31 AF XY: 0.229 AC XY: 16989 AN XY: 74230

African (AFR) AF: 0.159 AC: 6593 AN: 41492

American (AMR) AF: 0.264 AC: 4015 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3466

East Asian (EAS) AF: 0.366 AC: 1885 AN: 5150

South Asian (SAS) AF: 0.285 AC: 1375 AN: 4820

European-Finnish (FIN) AF: 0.205 AC: 2162 AN: 10544

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16774 AN: 67922

Other (OTH) AF: 0.235 AC: 496 AN: 2108

Alfa AF: 0.239 Hom.: 13476

Bravo AF: 0.225

Asia WGS AF: 0.311 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.45
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs17608635; hg19: chr4-45079676;