rs9892996

Variant names:

• chr17-75307136-G-A
• rs9892996

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 0.183 in 151,352 control chromosomes in the GnomAD database, including 2,695 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 0.18 (2695 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.24 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: 0.183 AC: 27613 AN: 151242 Hom.: 2680 Cov.: 30

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.0431

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.183 AC: 27654 AN: 151352 Hom.: 2695 Cov.: 30 AF XY: 0.182 AC XY: 13434 AN XY: 73916

African (AFR) AF: 0.154 AC: 6354 AN: 41280

American (AMR) AF: 0.151 AC: 2291 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1039 AN: 3464

East Asian (EAS) AF: 0.0428 AC: 221 AN: 5160

South Asian (SAS) AF: 0.252 AC: 1206 AN: 4782

European-Finnish (FIN) AF: 0.174 AC: 1810 AN: 10382

Middle Eastern (MID) AF: 0.279 AC: 81 AN: 290

European-Non Finnish (NFE) AF: 0.208 AC: 14127 AN: 67824

Other (OTH) AF: 0.208 AC: 437 AN: 2098

Alfa AF: 0.206 Hom.: 6488

Bravo AF: 0.176

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.37
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs9892996; hg19: chr17-73303217;