rs17085007

chr13-26957130-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 0.162 in 152,210 control chromosomes in the GnomAD database, including 2,242 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 0.16 (2242 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.268 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: 0.162 AC: 24627 AN: 152090 Hom.: 2243 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.162 AC: 24632 AN: 152210 Hom.: 2242 Cov.: 33 AF XY: 0.165 AC XY: 12268 AN XY: 74412

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.168

Alfa AF: 0.181 Hom.: 5892

Bravo AF: 0.159

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	8.2
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17085007; hg19: chr13-27531267;