4-42837718-A-G

Variant names:

• chr4-42837718-A-G
• rs1074454

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 0.824 in 152,146 control chromosomes in the GnomAD database, including 53,166 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 0.82 (53166 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.92 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: 0.825 AC: 125349 AN: 152028 Hom.: 53148 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.824 AC: 125415 AN: 152146 Hom.: 53166 Cov.: 31 AF XY: 0.828 AC XY: 61603 AN XY: 74366

African (AFR) AF: 0.602 AC: 24966 AN: 41446

American (AMR) AF: 0.878 AC: 13424 AN: 15292

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

East Asian (EAS) AF: 0.925 AC: 4784 AN: 5170

South Asian (SAS) AF: 0.943 AC: 4547 AN: 4822

European-Finnish (FIN) AF: 0.907 AC: 9610 AN: 10590

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61986 AN: 68032

Other (OTH) AF: 0.840 AC: 1777 AN: 2116

Alfa AF: 0.890 Hom.: 30604

Bravo AF: 0.811

Asia WGS AF: 0.903 AC: 3141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.42
DANN	Benign	0.70
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1074454; hg19: chr4-42839735;