chr4-54656321-G-T

Variant names:

• chr4-54656321-G-T
• rs6554199

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 0.538 in 151,900 control chromosomes in the GnomAD database, including 22,042 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 0.54 (22042 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81628 AN: 151782 Hom.: 22026 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.538 AC: 81688 AN: 151900 Hom.: 22042 Cov.: 32 AF XY: 0.537 AC XY: 39826 AN XY: 74232

African (AFR) AF: 0.532 AC: 22038 AN: 41404

American (AMR) AF: 0.556 AC: 8499 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1607 AN: 3466

East Asian (EAS) AF: 0.447 AC: 2300 AN: 5148

South Asian (SAS) AF: 0.538 AC: 2590 AN: 4816

European-Finnish (FIN) AF: 0.532 AC: 5610 AN: 10536

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.550 AC: 37337 AN: 67944

Other (OTH) AF: 0.519 AC: 1093 AN: 2104

Alfa AF: 0.531 Hom.: 10524

Bravo AF: 0.539

Asia WGS AF: 0.528 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs6554199; hg19: chr4-55522488;