chr4-124784789-G-C

Position:

• chr4-124784789-G-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 0.374 in 151,786 control chromosomes in the GnomAD database, including 10,815 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 0.37 (10815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 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: 0.374 AC: 56720 AN: 151670 Hom.: 10801 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.374 AC: 56769 AN: 151786 Hom.: 10815 Cov.: 32 AF XY: 0.380 AC XY: 28147 AN XY: 74150

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.370

Alfa AF: 0.216 Hom.: 488

Bravo AF: 0.368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2174623; hg19: chr4-125705944;