rs17176973

chr5-10811362-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0248 in 151,974 control chromosomes in the GnomAD database, including 77 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 0.025 (77 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0248 (3769/151974) while in subpopulation NFE AF= 0.0336 (2287/67972). AF 95% confidence interval is 0.0325. There are 77 homozygotes in gnomad4. There are 1862 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 77 gene

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: 0.0248 AC: 3772 AN: 151874 Hom.: 77 Cov.: 31

Gnomad AFR AF: 0.00614

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0281

Gnomad ASJ AF: 0.0628

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0337

Gnomad OTH AF: 0.0394

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

GnomAD4 genome AF: 0.0248 AC: 3769 AN: 151974 Hom.: 77 Cov.: 31 AF XY: 0.0251 AC XY: 1862 AN XY: 74248

Gnomad4 AFR AF: 0.00613

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0628

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0162

Gnomad4 FIN AF: 0.0374

Gnomad4 NFE AF: 0.0336

Gnomad4 OTH AF: 0.0390

Alfa AF: 0.0316 Hom.: 10

Bravo AF: 0.0233

Asia WGS AF: 0.00578 AC: 20 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	9.4
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17176973; hg19: chr5-10811474;