rs17161553

Variant names:

• chr5-100966102-T-C
• rs17161553

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 0.046 in 152,052 control chromosomes in the GnomAD database, including 376 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 0.046 (376 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.136 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: 0.0458 AC: 6965 AN: 151934 Hom.: 368 Cov.: 31

Gnomad AFR AF: 0.0879

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.00736

Gnomad SAS AF: 0.0134

Gnomad FIN AF: 0.0148

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.0355

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

GnomAD4 genome AF: 0.0460 AC: 6992 AN: 152052 Hom.: 376 Cov.: 31 AF XY: 0.0471 AC XY: 3499 AN XY: 74318

Gnomad4 AFR AF: 0.0879

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0205

Gnomad4 EAS AF: 0.00738

Gnomad4 SAS AF: 0.0137

Gnomad4 FIN AF: 0.0148

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.0351

Alfa AF: 0.0344 Hom.: 39

Bravo AF: 0.0585

Asia WGS AF: 0.0220 AC: 77 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	0.38
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17161553; hg19: chr5-100301806;