rs17763040

Variant names:

• chr13-33071247-A-G
• rs17763040

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 0.0955 in 152,304 control chromosomes in the GnomAD database, including 991 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 0.096 (991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 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: 0.0956 AC: 14549 AN: 152186 Hom.: 992 Cov.: 32

Gnomad AFR AF: 0.0260

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0955 AC: 14547 AN: 152304 Hom.: 991 Cov.: 32 AF XY: 0.0918 AC XY: 6834 AN XY: 74478

African (AFR) AF: 0.0259 AC: 1079 AN: 41582

American (AMR) AF: 0.105 AC: 1603 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3472

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.0369 AC: 178 AN: 4830

European-Finnish (FIN) AF: 0.105 AC: 1110 AN: 10614

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9665 AN: 67996

Other (OTH) AF: 0.111 AC: 234 AN: 2114

Alfa AF: 0.0869 Hom.: 258

Bravo AF: 0.0944

Asia WGS AF: 0.0180 AC: 62 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.67
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs17763040; hg19: chr13-33645384;