chr4-10124321-C-G

Position:

• chr4-10124321-C-G

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 0.111 in 152,214 control chromosomes in the GnomAD database, including 1,302 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 (1302 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16930 AN: 152096 Hom.: 1297 Cov.: 34

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.0972

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

GnomAD4 genome AF: 0.111 AC: 16956 AN: 152214 Hom.: 1302 Cov.: 34 AF XY: 0.115 AC XY: 8579 AN XY: 74420

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.0720

Gnomad4 NFE AF: 0.0669

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0853 Hom.: 74

Bravo AF: 0.121

Asia WGS AF: 0.251 AC: 872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516202; hg19: chr4-10125945;