9-12650996-C-G

Position:

• chr9-12650996-C-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 0.438 in 151,944 control chromosomes in the GnomAD database, including 18,542 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 0.44 (18542 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890

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 (NFE) allele frequency at 95% confidence interval = 0.628 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: 0.438 AC: 66507 AN: 151824 Hom.: 18545 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.438 AC: 66521 AN: 151944 Hom.: 18542 Cov.: 31 AF XY: 0.432 AC XY: 32108 AN XY: 74270

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.438

Alfa AF: 0.534 Hom.: 3037

Bravo AF: 0.400

Asia WGS AF: 0.139 AC: 486 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	0.47
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10809811; hg19: chr9-12650996;