9-21241450-G-T

Variant names:

• chr9-21241450-G-T
• rs12553763

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 0.215 in 152,082 control chromosomes in the GnomAD database, including 3,873 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 0.21 (3873 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 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: 0.215 AC: 32623 AN: 151964 Hom.: 3870 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.215 AC: 32656 AN: 152082 Hom.: 3873 Cov.: 33 AF XY: 0.215 AC XY: 15989 AN XY: 74326

African (AFR) AF: 0.275 AC: 11406 AN: 41494

American (AMR) AF: 0.253 AC: 3868 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3464

East Asian (EAS) AF: 0.398 AC: 2055 AN: 5166

South Asian (SAS) AF: 0.113 AC: 545 AN: 4828

European-Finnish (FIN) AF: 0.190 AC: 2010 AN: 10552

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11458 AN: 67986

Other (OTH) AF: 0.207 AC: 436 AN: 2108

Alfa AF: 0.114 Hom.: 191

Bravo AF: 0.225

Asia WGS AF: 0.247 AC: 860 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	0.14
DANN	Benign	0.21
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs12553763; hg19: chr9-21241449;