4-55126199-A-G

Variant names:

• chr4-55126199-A-G
• rs2071559

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 0.523 in 152,036 control chromosomes in the GnomAD database, including 21,357 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 0.52 (21357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.596
• Publications: 193 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 (AFR) allele frequency at 95% confidence interval = 0.635 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: 0.523 AC: 79475 AN: 151916 Hom.: 21350 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.523 AC: 79515 AN: 152036 Hom.: 21357 Cov.: 32 AF XY: 0.518 AC XY: 38534 AN XY: 74326

African (AFR) AF: 0.641 AC: 26586 AN: 41466

American (AMR) AF: 0.420 AC: 6423 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1885 AN: 3464

East Asian (EAS) AF: 0.336 AC: 1737 AN: 5162

South Asian (SAS) AF: 0.537 AC: 2589 AN: 4822

European-Finnish (FIN) AF: 0.432 AC: 4561 AN: 10568

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33965 AN: 67954

Other (OTH) AF: 0.496 AC: 1046 AN: 2108

Alfa AF: 0.505 Hom.: 83021

Bravo AF: 0.524

Asia WGS AF: 0.449 AC: 1564 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	1.4
DANN	Benign	0.22
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2071559; hg19: chr4-55992366;