rs2172745

chr5-158290898-C-Achr5-158290898-C-G

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 0.226 in 152,158 control chromosomes in the GnomAD database, including 4,071 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 0.23 (4071 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 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: 0.226 AC: 34383 AN: 152040 Hom.: 4073 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.226 AC: 34389 AN: 152158 Hom.: 4071 Cov.: 33 AF XY: 0.227 AC XY: 16903 AN XY: 74386

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.0774

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.258

Alfa AF: 0.244 Hom.: 6140

Bravo AF: 0.216

Asia WGS AF: 0.205 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	12
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2172745; hg19: chr5-157717906; COSMIC: COSV60221007;