4-19052136-G-A

Variant names:

• chr4-19052136-G-A
• rs207338

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 0.51 in 151,914 control chromosomes in the GnomAD database, including 20,106 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 0.51 (20106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.886
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.569 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: 0.510 AC: 77394 AN: 151796 Hom.: 20089 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.510 AC: 77456 AN: 151914 Hom.: 20106 Cov.: 32 AF XY: 0.507 AC XY: 37637 AN XY: 74242

African (AFR) AF: 0.566 AC: 23453 AN: 41414

American (AMR) AF: 0.579 AC: 8824 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3470

East Asian (EAS) AF: 0.424 AC: 2186 AN: 5152

South Asian (SAS) AF: 0.418 AC: 2013 AN: 4812

European-Finnish (FIN) AF: 0.428 AC: 4522 AN: 10554

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33172 AN: 67952

Other (OTH) AF: 0.507 AC: 1071 AN: 2112

Alfa AF: 0.496 Hom.: 15079

Bravo AF: 0.524

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.2
DANN	Benign	0.67
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs207338; hg19: chr4-19053759;