rs1333344

Variant names:

• chr9-109013944-G-A
• rs1333344

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 0.222 in 152,002 control chromosomes in the GnomAD database, including 4,494 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 0.22 (4494 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.293 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: 0.222 AC: 33714 AN: 151882 Hom.: 4490 Cov.: 33

Gnomad AFR AF: 0.0605

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.222 AC: 33728 AN: 152002 Hom.: 4494 Cov.: 33 AF XY: 0.224 AC XY: 16600 AN XY: 74260

African (AFR) AF: 0.0605 AC: 2512 AN: 41540

American (AMR) AF: 0.300 AC: 4590 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1067 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1462 AN: 5146

South Asian (SAS) AF: 0.192 AC: 925 AN: 4824

European-Finnish (FIN) AF: 0.299 AC: 3126 AN: 10456

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.284 AC: 19285 AN: 67960

Other (OTH) AF: 0.245 AC: 517 AN: 2108

Alfa AF: 0.256 Hom.: 14944

Bravo AF: 0.215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.5
DANN	Benign	0.93
PhyloP100		-0.080
PromoterAI		0.052	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1333344; hg19: chr9-111776224; COSMIC: COSV57702130;