rs17652284

Variant names:

• chr4-68357339-G-T
• rs17652284

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 0.043 in 152,246 control chromosomes in the GnomAD database, including 226 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 0.043 (226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0552 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: 0.0431 AC: 6550 AN: 152128 Hom.: 226 Cov.: 32

Gnomad AFR AF: 0.00910

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0398

Gnomad ASJ AF: 0.0884

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0935

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0567

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0430 AC: 6545 AN: 152246 Hom.: 226 Cov.: 32 AF XY: 0.0447 AC XY: 3330 AN XY: 74448

Gnomad4 AFR AF: 0.00907

Gnomad4 AMR AF: 0.0398

Gnomad4 ASJ AF: 0.0884

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.0935

Gnomad4 NFE AF: 0.0567

Gnomad4 OTH AF: 0.0411

Alfa AF: 0.0539 Hom.: 146

Bravo AF: 0.0388

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17652284; hg19: chr4-69223057;