4-124784789-G-C

Variant names:

• chr4-124784789-G-C
• rs2174623

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;