rs9896052

Variant names:

• chr17-75422781-A-C
• rs9896052

Your query was ambiguous. Multiple possible variants found:

• chr17-75422781-A-C
• chr17-75422781-A-T

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 0.507 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
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.165 AC: 6845 AN: 41452

American (AMR) AF: 0.465 AC: 7073 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1851 AN: 3468

East Asian (EAS) AF: 0.454 AC: 2346 AN: 5164

South Asian (SAS) AF: 0.521 AC: 2511 AN: 4822

European-Finnish (FIN) AF: 0.733 AC: 7737 AN: 10552

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46854 AN: 67962

Other (OTH) AF: 0.498 AC: 1051 AN: 2110

Alfa AF: 0.613 Hom.: 40942

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs9896052; hg19: chr17-73418862;