4-82419452-G-A

Variant names:

• chr4-82419452-G-A
• rs1559949

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 0.737 in 149,808 control chromosomes in the GnomAD database, including 43,673 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 0.74 (43673 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 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: 0.738 AC: 110415 AN: 149682 Hom.: 43658 Cov.: 26

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.737 AC: 110479 AN: 149808 Hom.: 43673 Cov.: 26 AF XY: 0.742 AC XY: 54135 AN XY: 72914

African (AFR) AF: 0.424 AC: 17376 AN: 40962

American (AMR) AF: 0.811 AC: 12126 AN: 14954

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2797 AN: 3448

East Asian (EAS) AF: 0.917 AC: 4519 AN: 4926

South Asian (SAS) AF: 0.832 AC: 3954 AN: 4750

European-Finnish (FIN) AF: 0.896 AC: 9033 AN: 10078

Middle Eastern (MID) AF: 0.769 AC: 223 AN: 290

European-Non Finnish (NFE) AF: 0.865 AC: 58292 AN: 67420

Other (OTH) AF: 0.758 AC: 1570 AN: 2072

Alfa AF: 0.828 Hom.: 105503

Bravo AF: 0.720

Asia WGS AF: 0.851 AC: 2960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.36
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs1559949; hg19: chr4-83340605;