rs10992471

Variant names:

• chr9-92797223-G-A
• rs10992471

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;