17-53232116-A-G

Variant names:

• chr17-53232116-A-G
• rs807072

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 0.568 in 151,768 control chromosomes in the GnomAD database, including 24,840 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 0.57 (24840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.644 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: 0.568 AC: 86171 AN: 151650 Hom.: 24820 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.568 AC: 86213 AN: 151768 Hom.: 24840 Cov.: 32 AF XY: 0.563 AC XY: 41752 AN XY: 74186

African (AFR) AF: 0.494 AC: 20456 AN: 41450

American (AMR) AF: 0.654 AC: 9959 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2045 AN: 3466

East Asian (EAS) AF: 0.358 AC: 1838 AN: 5140

South Asian (SAS) AF: 0.535 AC: 2574 AN: 4812

European-Finnish (FIN) AF: 0.544 AC: 5744 AN: 10558

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.614 AC: 41655 AN: 67816

Other (OTH) AF: 0.604 AC: 1272 AN: 2106

Alfa AF: 0.598 Hom.: 117276

Bravo AF: 0.572

Asia WGS AF: 0.438 AC: 1523 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.17
DANN	Benign	0.68
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs807072; hg19: chr17-51309477;