rs17070284

Variant names:

• chr13-78785289-C-T
• rs17070284

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.131 in 152,152 control chromosomes in the GnomAD database, including 1,464 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 0.13 (1464 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.55
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 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: 0.131 AC: 19844 AN: 152034 Hom.: 1459 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0881

Gnomad FIN AF: 0.0488

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0994

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.131 AC: 19864 AN: 152152 Hom.: 1464 Cov.: 33 AF XY: 0.128 AC XY: 9534 AN XY: 74388

African (AFR) AF: 0.194 AC: 8057 AN: 41492

American (AMR) AF: 0.166 AC: 2538 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3468

East Asian (EAS) AF: 0.112 AC: 582 AN: 5182

South Asian (SAS) AF: 0.0876 AC: 423 AN: 4830

European-Finnish (FIN) AF: 0.0488 AC: 516 AN: 10580

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0994 AC: 6761 AN: 68014

Other (OTH) AF: 0.125 AC: 265 AN: 2112

Alfa AF: 0.112 Hom.: 2324

Bravo AF: 0.145

Asia WGS AF: 0.112 AC: 386 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	23
DANN	Benign	0.79
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs17070284; hg19: chr13-79359424;