rs4836819

Variant names:

• chr9-120388175-A-G
• rs4836819

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 0.655 in 152,172 control chromosomes in the GnomAD database, including 33,180 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 0.66 (33180 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 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: 0.655 AC: 99671 AN: 152054 Hom.: 33161 Cov.: 34

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.655 AC: 99737 AN: 152172 Hom.: 33180 Cov.: 34 AF XY: 0.659 AC XY: 49048 AN XY: 74402

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.663

Alfa AF: 0.653 Hom.: 6120

Bravo AF: 0.653

Asia WGS AF: 0.752 AC: 2616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4836819; hg19: chr9-123150453;