chr4-122449232-G-A

Variant names:

• chr4-122449232-G-A
• rs1479923

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 0.248 in 152,062 control chromosomes in the GnomAD database, including 5,694 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 0.25 (5694 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37747 AN: 151944 Hom.: 5680 Cov.: 31

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.248 AC: 37781 AN: 152062 Hom.: 5694 Cov.: 31 AF XY: 0.254 AC XY: 18904 AN XY: 74320

African (AFR) AF: 0.0738 AC: 3064 AN: 41508

American (AMR) AF: 0.299 AC: 4560 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3470

East Asian (EAS) AF: 0.339 AC: 1749 AN: 5164

South Asian (SAS) AF: 0.505 AC: 2430 AN: 4812

European-Finnish (FIN) AF: 0.291 AC: 3078 AN: 10560

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.299 AC: 20306 AN: 67978

Other (OTH) AF: 0.302 AC: 637 AN: 2112

Alfa AF: 0.283 Hom.: 18948

Bravo AF: 0.237

Asia WGS AF: 0.422 AC: 1468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.47
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1479923; hg19: chr4-123370387;