chr4-10239039-T-C

Position:

• chr4-10239039-T-C

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 0.187 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.177

Alfa AF: 0.179 Hom.: 2560

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11734783; hg19: chr4-10240663;