chr4-54634059-C-A

Variant names:

• chr4-54634059-C-A
• rs6831020

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 0.204 in 152,114 control chromosomes in the GnomAD database, including 3,987 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 0.20 (3987 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30963 AN: 151996 Hom.: 3987 Cov.: 32

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.204 AC: 30963 AN: 152114 Hom.: 3987 Cov.: 32 AF XY: 0.200 AC XY: 14883 AN XY: 74334

African (AFR) AF: 0.0555 AC: 2303 AN: 41512

American (AMR) AF: 0.294 AC: 4488 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3470

East Asian (EAS) AF: 0.0706 AC: 366 AN: 5182

South Asian (SAS) AF: 0.160 AC: 772 AN: 4818

European-Finnish (FIN) AF: 0.233 AC: 2461 AN: 10560

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18889 AN: 67976

Other (OTH) AF: 0.218 AC: 461 AN: 2110

Alfa AF: 0.258 Hom.: 7790

Bravo AF: 0.205

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.6
DANN	Benign	0.80
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs6831020; hg19: chr4-55500226;