rs473367

Variant names:

• chr9-26256240-G-A
• rs473367

Your query was ambiguous. Multiple possible variants found:

• chr9-26256240-G-A
• chr9-26256240-G-C
• chr9-26256240-G-T

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 0.898 in 152,064 control chromosomes in the GnomAD database, including 61,831 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 0.90 (61831 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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: 0.899 AC: 136538 AN: 151948 Hom.: 61801 Cov.: 30

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.913

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

GnomAD4 genome AF: 0.898 AC: 136617 AN: 152064 Hom.: 61831 Cov.: 30 AF XY: 0.900 AC XY: 66867 AN XY: 74316

African (AFR) AF: 0.781 AC: 32370 AN: 41470

American (AMR) AF: 0.934 AC: 14266 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3063 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5119 AN: 5154

South Asian (SAS) AF: 0.971 AC: 4676 AN: 4818

European-Finnish (FIN) AF: 0.924 AC: 9774 AN: 10578

Middle Eastern (MID) AF: 0.904 AC: 264 AN: 292

European-Non Finnish (NFE) AF: 0.946 AC: 64290 AN: 67990

Other (OTH) AF: 0.912 AC: 1926 AN: 2112

Alfa AF: 0.919 Hom.: 10880

Bravo AF: 0.894

Asia WGS AF: 0.952 AC: 3308 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs473367; hg19: chr9-26256238; COSMIC: COSV69454722;