chr4-10239039-T-C

Variant names:

• chr4-10239039-T-C
• rs11734783

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 0.187 in 152,166 control chromosomes in the GnomAD database, including 2,757 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 0.19 (2757 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.216 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: 0.186 AC: 28354 AN: 152048 Hom.: 2749 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.187 AC: 28381 AN: 152166 Hom.: 2757 Cov.: 33 AF XY: 0.187 AC XY: 13929 AN XY: 74398

African (AFR) AF: 0.215 AC: 8916 AN: 41492

American (AMR) AF: 0.222 AC: 3395 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 741 AN: 3470

East Asian (EAS) AF: 0.138 AC: 712 AN: 5178

South Asian (SAS) AF: 0.161 AC: 776 AN: 4822

European-Finnish (FIN) AF: 0.172 AC: 1826 AN: 10596

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11469 AN: 67998

Other (OTH) AF: 0.177 AC: 374 AN: 2112

Alfa AF: 0.183 Hom.: 3652

Bravo AF: 0.191

Asia WGS AF: 0.140 AC: 488 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	5.3
DANN	Benign	0.74
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs11734783; hg19: chr4-10240663;