17-13655763-A-G

Variant names:

• chr17-13655763-A-G
• rs10521233

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 0.0661 in 152,252 control chromosomes in the GnomAD database, including 361 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 0.066 (361 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 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: 0.0660 AC: 10042 AN: 152134 Hom.: 361 Cov.: 32

Gnomad AFR AF: 0.0422

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0806

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0529

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0661 AC: 10066 AN: 152252 Hom.: 361 Cov.: 32 AF XY: 0.0680 AC XY: 5058 AN XY: 74434

Gnomad4 AFR AF: 0.0425

Gnomad4 AMR AF: 0.0807

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0541

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0671

Gnomad4 OTH AF: 0.0582

Alfa AF: 0.0649 Hom.: 411

Bravo AF: 0.0655

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.2
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521233; hg19: chr17-13559080;