rs4838140

Variant names:

• chr9-124247835-T-C
• rs4838140

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 0.171 in 152,152 control chromosomes in the GnomAD database, including 2,277 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 0.17 (2277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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: 0.171 AC: 25973 AN: 152034 Hom.: 2276 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0932

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.171 AC: 26006 AN: 152152 Hom.: 2277 Cov.: 32 AF XY: 0.172 AC XY: 12811 AN XY: 74376

African (AFR) AF: 0.178 AC: 7382 AN: 41546

American (AMR) AF: 0.139 AC: 2130 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3464

East Asian (EAS) AF: 0.177 AC: 914 AN: 5174

South Asian (SAS) AF: 0.0932 AC: 450 AN: 4826

European-Finnish (FIN) AF: 0.180 AC: 1902 AN: 10586

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11865 AN: 67966

Other (OTH) AF: 0.156 AC: 327 AN: 2102

Alfa AF: 0.169 Hom.: 9421

Bravo AF: 0.165

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4838140; hg19: chr9-127010114;