rs17176973

Variant names:

• chr5-10811362-C-G
• rs17176973

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 77 gene

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: 0.0248 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

African (AFR) AF: 0.00613 AC: 254 AN: 41466

American (AMR) AF: 0.0280 AC: 428 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0628 AC: 218 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.0162 AC: 78 AN: 4804

European-Finnish (FIN) AF: 0.0374 AC: 393 AN: 10502

Middle Eastern (MID) AF: 0.0479 AC: 14 AN: 292

European-Non Finnish (NFE) AF: 0.0336 AC: 2287 AN: 67972

Other (OTH) AF: 0.0390 AC: 82 AN: 2104

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
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs17176973; hg19: chr5-10811474;