4-128775066-A-G

Variant names:

• chr4-128775066-A-G
• rs1974942

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.887

Gnomad4 OTH AF: 0.779

Alfa AF: 0.825 Hom.: 6788

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1974942; hg19: chr4-129696221;