chr5-173208137-A-G

Variant names:

• chr5-173208137-A-G
• rs17075700

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 0.447 in 152,034 control chromosomes in the GnomAD database, including 17,533 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 0.45 (17533 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.742
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 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: 0.447 AC: 67895 AN: 151916 Hom.: 17482 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.447 AC: 68008 AN: 152034 Hom.: 17533 Cov.: 33 AF XY: 0.444 AC XY: 33001 AN XY: 74328

African (AFR) AF: 0.713 AC: 29565 AN: 41450

American (AMR) AF: 0.327 AC: 4986 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1434 AN: 3466

East Asian (EAS) AF: 0.144 AC: 746 AN: 5172

South Asian (SAS) AF: 0.456 AC: 2202 AN: 4826

European-Finnish (FIN) AF: 0.410 AC: 4334 AN: 10562

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23356 AN: 67966

Other (OTH) AF: 0.448 AC: 948 AN: 2116

Alfa AF: 0.348 Hom.: 1830

Bravo AF: 0.451

Asia WGS AF: 0.393 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.18
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs17075700; hg19: chr5-172635140;