chr9-26009634-A-G

Variant names:

• chr9-26009634-A-G
• rs1412451

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 0.323 in 151,738 control chromosomes in the GnomAD database, including 8,676 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 0.32 (8676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 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: 0.323 AC: 48991 AN: 151622 Hom.: 8660 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.323 AC: 49043 AN: 151738 Hom.: 8676 Cov.: 32 AF XY: 0.322 AC XY: 23881 AN XY: 74142

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.305

Alfa AF: 0.297 Hom.: 3665

Bravo AF: 0.316

Asia WGS AF: 0.316 AC: 1090 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1412451; hg19: chr9-26009632;