rs4550901

Positions:

• chr4-154580381-A-C
• chr4-154580381-A-G
• chr4-154580381-A-T

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 0.904 in 152,016 control chromosomes in the GnomAD database, including 62,337 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 0.90 (62337 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.51

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137343 AN: 151898 Hom.: 62286 Cov.: 30

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.904 AC: 137451 AN: 152016 Hom.: 62337 Cov.: 30 AF XY: 0.902 AC XY: 67022 AN XY: 74288

Gnomad4 AFR AF: 0.978

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.898

Alfa AF: 0.867 Hom.: 7604

Bravo AF: 0.912

Asia WGS AF: 0.889 AC: 3089 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	0.11
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4550901; hg19: chr4-155501533;