rs9892365

Positions:

• chr17-61414023-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 0.711 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.681

Alfa AF: 0.693 Hom.: 6471

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9892365; hg19: chr17-59491384;