9-12460256-A-G

Variant names:

• chr9-12460256-A-G
• rs4008031

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.335 in 151,998 control chromosomes in the GnomAD database, including 8,675 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 0.33 (8675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 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: 0.335 AC: 50816 AN: 151880 Hom.: 8662 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.335 AC: 50855 AN: 151998 Hom.: 8675 Cov.: 32 AF XY: 0.334 AC XY: 24800 AN XY: 74302

African (AFR) AF: 0.339 AC: 14043 AN: 41466

American (AMR) AF: 0.284 AC: 4331 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1113 AN: 3470

East Asian (EAS) AF: 0.150 AC: 774 AN: 5164

South Asian (SAS) AF: 0.276 AC: 1331 AN: 4822

European-Finnish (FIN) AF: 0.411 AC: 4335 AN: 10542

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23732 AN: 67958

Other (OTH) AF: 0.336 AC: 707 AN: 2104

Alfa AF: 0.337 Hom.: 36346

Bravo AF: 0.324

Asia WGS AF: 0.211 AC: 733 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	1.5
DANN	Benign	0.47
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4008031; hg19: chr9-12460256;