rs4837752

Variant names:

• chr9-120294359-G-A
• rs4837752

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 0.107 in 152,136 control chromosomes in the GnomAD database, including 1,261 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 0.11 (1261 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 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: 0.107 AC: 16313 AN: 152018 Hom.: 1254 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0483

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0520

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.107 AC: 16351 AN: 152136 Hom.: 1261 Cov.: 32 AF XY: 0.110 AC XY: 8198 AN XY: 74378

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.0522

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0483

Gnomad4 NFE AF: 0.0520

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0716 Hom.: 1319

Bravo AF: 0.123

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.62
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4837752; hg19: chr9-123056637;