9-119150811-G-A

Variant names:

• chr9-119150811-G-A
• rs1412521

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 0.519 in 152,078 control chromosomes in the GnomAD database, including 24,768 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 0.52 (24768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 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: 0.520 AC: 78997 AN: 151960 Hom.: 24766 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.519 AC: 78997 AN: 152078 Hom.: 24768 Cov.: 32 AF XY: 0.524 AC XY: 38988 AN XY: 74340

African (AFR) AF: 0.142 AC: 5875 AN: 41498

American (AMR) AF: 0.584 AC: 8923 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2318 AN: 3470

East Asian (EAS) AF: 0.634 AC: 3270 AN: 5156

South Asian (SAS) AF: 0.551 AC: 2660 AN: 4824

European-Finnish (FIN) AF: 0.763 AC: 8074 AN: 10584

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46032 AN: 67964

Other (OTH) AF: 0.545 AC: 1150 AN: 2112

Alfa AF: 0.536 Hom.: 4505

Bravo AF: 0.493

Asia WGS AF: 0.556 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs1412521; hg19: chr9-121913089;