rs1412451

Variant names:

• chr9-26009634-A-G
• rs1412451

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 0.323 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.462 AC: 19123 AN: 41398

American (AMR) AF: 0.193 AC: 2938 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3472

East Asian (EAS) AF: 0.208 AC: 1068 AN: 5132

South Asian (SAS) AF: 0.468 AC: 2251 AN: 4814

European-Finnish (FIN) AF: 0.270 AC: 2827 AN: 10482

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.278 AC: 18883 AN: 67912

Other (OTH) AF: 0.305 AC: 643 AN: 2108

Alfa AF: 0.297 Hom.: 4006

Bravo AF: 0.316

Asia WGS AF: 0.316 AC: 1090 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.54
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1412451; hg19: chr9-26009632;