rs733646

Variant names:

• chr17-66829931-A-G
• rs733646

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 0.09 in 152,194 control chromosomes in the GnomAD database, including 809 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 0.090 (809 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 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: 0.0900 AC: 13694 AN: 152076 Hom.: 808 Cov.: 32

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.00828

Gnomad SAS AF: 0.0340

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.0894

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

GnomAD4 genome AF: 0.0900 AC: 13695 AN: 152194 Hom.: 809 Cov.: 32 AF XY: 0.0895 AC XY: 6660 AN XY: 74410

African (AFR) AF: 0.0223 AC: 927 AN: 41546

American (AMR) AF: 0.0862 AC: 1318 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3468

East Asian (EAS) AF: 0.00830 AC: 43 AN: 5180

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4822

European-Finnish (FIN) AF: 0.154 AC: 1628 AN: 10582

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8968 AN: 67994

Other (OTH) AF: 0.0889 AC: 188 AN: 2114

Alfa AF: 0.115 Hom.: 832

Bravo AF: 0.0818

Asia WGS AF: 0.0280 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	18
DANN	Benign	0.71
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs733646; hg19: chr17-64826049;