9-79807917-A-G

Variant names:

• chr9-79807917-A-G
• rs10512091

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 0.803 in 152,074 control chromosomes in the GnomAD database, including 49,370 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 0.80 (49370 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 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: 0.803 AC: 121968 AN: 151956 Hom.: 49337 Cov.: 30

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.803 AC: 122049 AN: 152074 Hom.: 49370 Cov.: 30 AF XY: 0.799 AC XY: 59385 AN XY: 74350

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.800

Alfa AF: 0.789 Hom.: 23788

Bravo AF: 0.802

Asia WGS AF: 0.716 AC: 2491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512091; hg19: chr9-82422832; COSMIC: COSV60364153;