4-54655993-G-A

Variant names:

• chr4-54655993-G-A
• rs6554198

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 0.624 in 151,846 control chromosomes in the GnomAD database, including 30,148 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 0.62 (30148 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 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: 0.624 AC: 94689 AN: 151732 Hom.: 30106 Cov.: 31

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.624 AC: 94782 AN: 151846 Hom.: 30148 Cov.: 31 AF XY: 0.622 AC XY: 46164 AN XY: 74212

African (AFR) AF: 0.753 AC: 31193 AN: 41412

American (AMR) AF: 0.605 AC: 9225 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1727 AN: 3470

East Asian (EAS) AF: 0.448 AC: 2310 AN: 5162

South Asian (SAS) AF: 0.555 AC: 2669 AN: 4810

European-Finnish (FIN) AF: 0.598 AC: 6282 AN: 10506

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.581 AC: 39491 AN: 67922

Other (OTH) AF: 0.580 AC: 1223 AN: 2108

Alfa AF: 0.591 Hom.: 34460

Bravo AF: 0.631

Asia WGS AF: 0.553 AC: 1919 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.67
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs6554198; hg19: chr4-55522160;