rs17702447

Variant names:

• chr5-180741265-T-C
• rs17702447

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 0.11 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
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.146 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: 0.110 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

African (AFR) AF: 0.0276 AC: 1146 AN: 41540

American (AMR) AF: 0.124 AC: 1900 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3466

East Asian (EAS) AF: 0.108 AC: 563 AN: 5192

South Asian (SAS) AF: 0.149 AC: 717 AN: 4810

European-Finnish (FIN) AF: 0.103 AC: 1095 AN: 10588

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.149 AC: 10120 AN: 67968

Other (OTH) AF: 0.128 AC: 271 AN: 2110

Alfa AF: 0.137 Hom.: 3639

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
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs17702447; hg19: chr5-180168265;