chr17-13655763-A-G

Variant names:

• chr17-13655763-A-G
• rs10521233

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 0.0661 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0425 AC: 1767 AN: 41552

American (AMR) AF: 0.0807 AC: 1234 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3470

East Asian (EAS) AF: 0.136 AC: 703 AN: 5178

South Asian (SAS) AF: 0.0541 AC: 261 AN: 4820

European-Finnish (FIN) AF: 0.114 AC: 1205 AN: 10602

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0671 AC: 4562 AN: 68024

Other (OTH) AF: 0.0582 AC: 123 AN: 2112

Alfa AF: 0.0645 Hom.: 1044

Bravo AF: 0.0655

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.2
DANN	Benign	0.46
PhyloP100		-0.010

Splicing

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

Other links and lift over

dbSNP: rs10521233; hg19: chr17-13559080;