4-128775066-A-G

Variant names:

• chr4-128775066-A-G
• rs1974942

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 0.779 in 152,184 control chromosomes in the GnomAD database, including 47,292 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 0.78 (47292 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.881 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: 0.780 AC: 118569 AN: 152066 Hom.: 47306 Cov.: 33

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.779 AC: 118589 AN: 152184 Hom.: 47292 Cov.: 33 AF XY: 0.775 AC XY: 57678 AN XY: 74392

African (AFR) AF: 0.619 AC: 25703 AN: 41492

American (AMR) AF: 0.721 AC: 11023 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2593 AN: 3472

East Asian (EAS) AF: 0.655 AC: 3396 AN: 5182

South Asian (SAS) AF: 0.764 AC: 3689 AN: 4828

European-Finnish (FIN) AF: 0.860 AC: 9100 AN: 10586

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60352 AN: 68026

Other (OTH) AF: 0.779 AC: 1645 AN: 2112

Alfa AF: 0.832 Hom.: 86034

Bravo AF: 0.760

Asia WGS AF: 0.669 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.78
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1974942; hg19: chr4-129696221;