5-175547573-A-G

Variant names:

• chr5-175547573-A-G
• rs10476160

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.299 in 152,026 control chromosomes in the GnomAD database, including 8,505 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 0.30 (8505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45397 AN: 151908 Hom.: 8472 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.299 AC: 45482 AN: 152026 Hom.: 8505 Cov.: 32 AF XY: 0.297 AC XY: 22039 AN XY: 74320

African (AFR) AF: 0.545 AC: 22565 AN: 41432

American (AMR) AF: 0.245 AC: 3749 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 789 AN: 3472

East Asian (EAS) AF: 0.241 AC: 1242 AN: 5160

South Asian (SAS) AF: 0.180 AC: 869 AN: 4816

European-Finnish (FIN) AF: 0.186 AC: 1970 AN: 10584

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.199 AC: 13521 AN: 67968

Other (OTH) AF: 0.291 AC: 613 AN: 2110

Alfa AF: 0.225 Hom.: 18773

Bravo AF: 0.316

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.52
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10476160; hg19: chr5-174974576;