rs17770015

Variant names:

• chr10-113479005-C-G
• rs17770015

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 0.0683 in 152,200 control chromosomes in the GnomAD database, including 416 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 0.068 (416 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0897 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: 0.0683 AC: 10390 AN: 152082 Hom.: 414 Cov.: 33

Gnomad AFR AF: 0.0355

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0472

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.00616

Gnomad SAS AF: 0.0787

Gnomad FIN AF: 0.0892

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.0618

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

GnomAD4 genome AF: 0.0683 AC: 10400 AN: 152200 Hom.: 416 Cov.: 33 AF XY: 0.0684 AC XY: 5093 AN XY: 74418

Gnomad4 AFR AF: 0.0354

Gnomad4 AMR AF: 0.0471

Gnomad4 ASJ AF: 0.0901

Gnomad4 EAS AF: 0.00618

Gnomad4 SAS AF: 0.0792

Gnomad4 FIN AF: 0.0892

Gnomad4 NFE AF: 0.0916

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0831 Hom.: 78

Bravo AF: 0.0629

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.2
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17770015; hg19: chr10-115238764;