chr9-122369409-C-T

Variant names:

• chr9-122369409-C-T
• rs1330344

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 0.695 in 152,150 control chromosomes in the GnomAD database, including 37,891 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 0.69 (37891 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 43 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 = 0.783 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: 0.695 AC: 105699 AN: 152032 Hom.: 37891 Cov.: 33

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.695 AC: 105733 AN: 152150 Hom.: 37891 Cov.: 33 AF XY: 0.693 AC XY: 51546 AN XY: 74384

African (AFR) AF: 0.522 AC: 21673 AN: 41504

American (AMR) AF: 0.777 AC: 11885 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2677 AN: 3472

East Asian (EAS) AF: 0.572 AC: 2950 AN: 5154

South Asian (SAS) AF: 0.608 AC: 2932 AN: 4820

European-Finnish (FIN) AF: 0.712 AC: 7540 AN: 10592

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.789 AC: 53624 AN: 67998

Other (OTH) AF: 0.705 AC: 1488 AN: 2112

Alfa AF: 0.726 Hom.: 28252

Bravo AF: 0.696

Asia WGS AF: 0.573 AC: 1996 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	2.9
DANN	Benign	0.58
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs1330344; hg19: chr9-125131688;