9-133320327-T-G

Variant names:

• chr9-133320327-T-G
• rs493014

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 0.375 in 151,800 control chromosomes in the GnomAD database, including 12,130 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 0.37 (12130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 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: 0.374 AC: 56786 AN: 151710 Hom.: 12101 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.375 AC: 56867 AN: 151800 Hom.: 12130 Cov.: 32 AF XY: 0.371 AC XY: 27522 AN XY: 74130

African (AFR) AF: 0.580 AC: 24056 AN: 41448

American (AMR) AF: 0.231 AC: 3528 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3470

East Asian (EAS) AF: 0.101 AC: 520 AN: 5144

South Asian (SAS) AF: 0.238 AC: 1142 AN: 4806

European-Finnish (FIN) AF: 0.383 AC: 4004 AN: 10442

Middle Eastern (MID) AF: 0.226 AC: 66 AN: 292

European-Non Finnish (NFE) AF: 0.317 AC: 21505 AN: 67934

Other (OTH) AF: 0.323 AC: 676 AN: 2096

Alfa AF: 0.283 Hom.: 1835

Bravo AF: 0.369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs493014; hg19: chr9-136187163;