rs17702447

chr5-180741265-T-C

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 0.11 in 152,158 control chromosomes in the GnomAD database, including 1,099 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 0.11 (1099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.146 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: 0.110 AC: 16674 AN: 152040 Hom.: 1097 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.110 AC: 16679 AN: 152158 Hom.: 1099 Cov.: 32 AF XY: 0.109 AC XY: 8075 AN XY: 74384

Gnomad4 AFR AF: 0.0276

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.128

Alfa AF: 0.147 Hom.: 2638

Bravo AF: 0.106

Asia WGS AF: 0.145 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.7
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17702447; hg19: chr5-180168265;