chr4-124784789-G-C

Variant names:

• chr4-124784789-G-C
• rs2174623

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 0.374 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.379 AC: 15683 AN: 41400

American (AMR) AF: 0.375 AC: 5716 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1476 AN: 3470

East Asian (EAS) AF: 0.638 AC: 3273 AN: 5130

South Asian (SAS) AF: 0.467 AC: 2244 AN: 4806

European-Finnish (FIN) AF: 0.414 AC: 4350 AN: 10502

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22877 AN: 67920

Other (OTH) AF: 0.370 AC: 780 AN: 2106

Alfa AF: 0.216 Hom.: 488

Bravo AF: 0.368

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.54
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2174623; hg19: chr4-125705944;