rs807072

Positions:

• chr17-53232116-A-G

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 0.568 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.604

Alfa AF: 0.607 Hom.: 58117

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs807072; hg19: chr17-51309477;