rs1408799

chr9-12672097-T-C

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 0.505 in 151,638 control chromosomes in the GnomAD database, including 22,910 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 0.51 (22910 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76584 AN: 151520 Hom.: 22904 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.505 AC: 76614 AN: 151638 Hom.: 22910 Cov.: 32 AF XY: 0.494 AC XY: 36586 AN XY: 74078

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.519

Alfa AF: 0.624 Hom.: 61109

Bravo AF: 0.475

Asia WGS AF: 0.160 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.11
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1408799; hg19: chr9-12672097; COSMIC: COSV60331987;