chr9-131572909-G-A

Variant names:

• chr9-131572909-G-A
• rs4740283

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 0.869 in 152,294 control chromosomes in the GnomAD database, including 57,656 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 0.87 (57656 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 12 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 (AFR) allele frequency at 95% confidence interval = 0.93 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: 0.869 AC: 132208 AN: 152176 Hom.: 57597 Cov.: 33

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.869 AC: 132326 AN: 152294 Hom.: 57656 Cov.: 33 AF XY: 0.869 AC XY: 64726 AN XY: 74458

African (AFR) AF: 0.938 AC: 38998 AN: 41568

American (AMR) AF: 0.852 AC: 13022 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2849 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4118 AN: 5180

South Asian (SAS) AF: 0.823 AC: 3969 AN: 4822

European-Finnish (FIN) AF: 0.881 AC: 9355 AN: 10614

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57174 AN: 68032

Other (OTH) AF: 0.859 AC: 1817 AN: 2116

Alfa AF: 0.841 Hom.: 82734

Bravo AF: 0.869

Asia WGS AF: 0.839 AC: 2918 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	1.5
DANN	Benign	0.38
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4740283; hg19: chr9-134448296;