rs9892365

Variant names:

• chr17-61414023-A-G
• rs9892365

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 0.711 in 151,822 control chromosomes in the GnomAD database, including 38,834 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 0.71 (38834 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 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: 0.711 AC: 107890 AN: 151702 Hom.: 38781 Cov.: 29

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.711 AC: 108005 AN: 151822 Hom.: 38834 Cov.: 29 AF XY: 0.714 AC XY: 52944 AN XY: 74194

African (AFR) AF: 0.811 AC: 33544 AN: 41378

American (AMR) AF: 0.663 AC: 10108 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2439 AN: 3470

East Asian (EAS) AF: 0.693 AC: 3568 AN: 5152

South Asian (SAS) AF: 0.620 AC: 2968 AN: 4790

European-Finnish (FIN) AF: 0.738 AC: 7780 AN: 10542

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45339 AN: 67922

Other (OTH) AF: 0.681 AC: 1439 AN: 2112

Alfa AF: 0.685 Hom.: 48846

Bravo AF: 0.712

Asia WGS AF: 0.658 AC: 2292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	14
DANN	Benign	0.73
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs9892365; hg19: chr17-59491384;