rs549467

Variant names:

• chr4-98251081-G-T
• rs549467

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 0.934 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.976 AC: 40584 AN: 41574

American (AMR) AF: 0.932 AC: 14261 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2636 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5174 AN: 5180

South Asian (SAS) AF: 0.963 AC: 4649 AN: 4828

European-Finnish (FIN) AF: 0.943 AC: 10006 AN: 10610

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61977 AN: 68044

Other (OTH) AF: 0.897 AC: 1890 AN: 2108

Alfa AF: 0.925 Hom.: 49694

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs549467; hg19: chr4-99172232;