rs17085007

Variant names:

• chr13-26957130-T-C
• rs17085007

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 0.162 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
• Publications: 61 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.101 AC: 4177 AN: 41542

American (AMR) AF: 0.178 AC: 2721 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 556 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1197 AN: 5176

South Asian (SAS) AF: 0.280 AC: 1350 AN: 4814

European-Finnish (FIN) AF: 0.173 AC: 1836 AN: 10592

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12062 AN: 68008

Other (OTH) AF: 0.168 AC: 354 AN: 2112

Alfa AF: 0.177 Hom.: 11859

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
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs17085007; hg19: chr13-27531267;