rs4836817

Variant names:

• chr9-120373094-T-C
• rs4836817

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 0.757 in 151,952 control chromosomes in the GnomAD database, including 44,387 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 0.76 (44387 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 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: 0.757 AC: 114907 AN: 151836 Hom.: 44331 Cov.: 32

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.757 AC: 115021 AN: 151952 Hom.: 44387 Cov.: 32 AF XY: 0.755 AC XY: 56109 AN XY: 74280

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.750

Alfa AF: 0.727 Hom.: 11665

Bravo AF: 0.775

Asia WGS AF: 0.798 AC: 2704 AN: 3392

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4836817; hg19: chr9-123135372;