rs17024555

Variant names:

• chr4-95779498-C-T
• rs17024555

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 0.159 in 151,878 control chromosomes in the GnomAD database, including 5,272 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 0.16 (5272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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: 0.158 AC: 24027 AN: 151760 Hom.: 5247 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0642

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0198

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0271

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.159 AC: 24098 AN: 151878 Hom.: 5272 Cov.: 32 AF XY: 0.154 AC XY: 11463 AN XY: 74248

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.0640

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.0242

Gnomad4 SAS AF: 0.0152

Gnomad4 FIN AF: 0.0198

Gnomad4 NFE AF: 0.0271

Gnomad4 OTH AF: 0.116

Alfa AF: 0.105 Hom.: 380

Bravo AF: 0.177

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17024555; hg19: chr4-96700649;