rs4550901

Variant names:

• chr4-154580381-A-C
• rs4550901

Your query was ambiguous. Multiple possible variants found:

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

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 0.904 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.978 AC: 40570 AN: 41468

American (AMR) AF: 0.887 AC: 13548 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2787 AN: 3470

East Asian (EAS) AF: 0.943 AC: 4864 AN: 5158

South Asian (SAS) AF: 0.857 AC: 4122 AN: 4808

European-Finnish (FIN) AF: 0.854 AC: 9009 AN: 10548

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59582 AN: 67982

Other (OTH) AF: 0.898 AC: 1896 AN: 2112

Alfa AF: 0.877 Hom.: 15897

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
PhyloP100		-4.5

Splicing

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

Other links and lift over

dbSNP: rs4550901; hg19: chr4-155501533;