4-180766439-A-G

Variant names:

• chr4-180766439-A-G
• rs2545258

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 0.71 in 152,090 control chromosomes in the GnomAD database, including 41,915 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 0.71 (41915 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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 = 0.866 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: 0.710 AC: 107908 AN: 151972 Hom.: 41914 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.710 AC: 107942 AN: 152090 Hom.: 41915 Cov.: 32 AF XY: 0.707 AC XY: 52583 AN XY: 74344

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.731

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.769

Alfa AF: 0.790 Hom.: 12107

Bravo AF: 0.697

Asia WGS AF: 0.778 AC: 2706 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	0.021
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2545258; hg19: chr4-181687592;