rs17161553

chr5-100966102-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;