rs4837752

Variant names:

• chr9-120294359-G-A
• rs4837752

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 0.107 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.168 AC: 6983 AN: 41464

American (AMR) AF: 0.185 AC: 2826 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0522 AC: 181 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1363 AN: 5168

South Asian (SAS) AF: 0.149 AC: 716 AN: 4818

European-Finnish (FIN) AF: 0.0483 AC: 513 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0520 AC: 3534 AN: 68008

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.0814 Hom.: 2684

Bravo AF: 0.123

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.62
DANN	Benign	0.57
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs4837752; hg19: chr9-123056637;