rs549467

chr4-98251081-G-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 0.934 in 152,330 control chromosomes in the GnomAD database, including 66,545 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 0.93 (66545 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.934 AC: 142124 AN: 152212 Hom.: 66486 Cov.: 33

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.963

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.934 AC: 142242 AN: 152330 Hom.: 66545 Cov.: 33 AF XY: 0.935 AC XY: 69689 AN XY: 74494

Gnomad4 AFR AF: 0.976

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.963

Gnomad4 FIN AF: 0.943

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.897

Alfa AF: 0.917 Hom.: 29441

Bravo AF: 0.934

Asia WGS AF: 0.979 AC: 3404 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	1.1
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs549467; hg19: chr4-99172232;