rs10992471

Positions:

• chr9-92797223-G-A

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 0.448 in 151,988 control chromosomes in the GnomAD database, including 16,694 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 0.45 (16694 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67952 AN: 151870 Hom.: 16666 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.0988

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.448 AC: 68016 AN: 151988 Hom.: 16694 Cov.: 31 AF XY: 0.440 AC XY: 32661 AN XY: 74270

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.0993

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.434

Alfa AF: 0.410 Hom.: 24192

Bravo AF: 0.455

Asia WGS AF: 0.206 AC: 717 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	0.88
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10992471; hg19: chr9-95559505;