rs17070284

chr13-78785289-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0876

Gnomad4 FIN AF: 0.0488

Gnomad4 NFE AF: 0.0994

Gnomad4 OTH AF: 0.125

Alfa AF: 0.105 Hom.: 1368

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17070284; hg19: chr13-79359424;