rs9896052

chr17-75422781-A-Cchr17-75422781-A-T

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 0.507 in 151,958 control chromosomes in the GnomAD database, including 23,568 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 0.51 (23568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.684 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: 0.508 AC: 77076 AN: 151840 Hom.: 23573 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.507 AC: 77061 AN: 151958 Hom.: 23568 Cov.: 32 AF XY: 0.509 AC XY: 37790 AN XY: 74254

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.498

Alfa AF: 0.634 Hom.: 33914

Bravo AF: 0.471

Asia WGS AF: 0.427 AC: 1487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.7
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9896052; hg19: chr17-73418862;