rs17608635

chr4-45077659-G-A

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 0.226 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.226 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

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.235

Alfa AF: 0.244 Hom.: 8034

Bravo AF: 0.225

Asia WGS AF: 0.311 AC: 1085 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.0
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17608635; hg19: chr4-45079676;