4-42838021-A-G

Variant names:

• chr4-42838021-A-G
• rs1074453

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 0.83 in 152,196 control chromosomes in the GnomAD database, including 53,676 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 0.83 (53676 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126212 AN: 152078 Hom.: 53659 Cov.: 33

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.830 AC: 126277 AN: 152196 Hom.: 53676 Cov.: 33 AF XY: 0.834 AC XY: 62041 AN XY: 74424

African (AFR) AF: 0.621 AC: 25745 AN: 41450

American (AMR) AF: 0.879 AC: 13451 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3201 AN: 3472

East Asian (EAS) AF: 0.925 AC: 4802 AN: 5190

South Asian (SAS) AF: 0.944 AC: 4559 AN: 4828

European-Finnish (FIN) AF: 0.908 AC: 9631 AN: 10610

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61986 AN: 68030

Other (OTH) AF: 0.843 AC: 1781 AN: 2112

Alfa AF: 0.890 Hom.: 30632

Bravo AF: 0.817

Asia WGS AF: 0.906 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1074453; hg19: chr4-42840038;