rs4740283

Positions:

• chr9-131572909-G-A
• chr9-131572909-G-C
• chr9-131572909-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.821

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.859

Alfa AF: 0.837 Hom.: 62818

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4740283; hg19: chr9-134448296;