4-126314560-A-C

Variant names:

• chr4-126314560-A-C
• rs1320244

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 0.591 in 151,894 control chromosomes in the GnomAD database, including 27,001 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 0.59 (27001 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89704 AN: 151776 Hom.: 26962 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.591 AC: 89799 AN: 151894 Hom.: 27001 Cov.: 32 AF XY: 0.587 AC XY: 43576 AN XY: 74226

African (AFR) AF: 0.702 AC: 29091 AN: 41458

American (AMR) AF: 0.522 AC: 7964 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2130 AN: 3466

East Asian (EAS) AF: 0.399 AC: 2058 AN: 5154

South Asian (SAS) AF: 0.611 AC: 2941 AN: 4816

European-Finnish (FIN) AF: 0.544 AC: 5736 AN: 10550

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37910 AN: 67890

Other (OTH) AF: 0.607 AC: 1282 AN: 2112

Alfa AF: 0.566 Hom.: 104126

Bravo AF: 0.590

Asia WGS AF: 0.520 AC: 1807 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.55
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1320244; hg19: chr4-127235715;