chr4-54612519-G-A

Variant names:

• chr4-54612519-G-A
• rs17827152

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 0.177 in 151,976 control chromosomes in the GnomAD database, including 2,964 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 0.18 (2964 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 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: 0.177 AC: 26880 AN: 151860 Hom.: 2961 Cov.: 31

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0720

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.177 AC: 26888 AN: 151976 Hom.: 2964 Cov.: 31 AF XY: 0.179 AC XY: 13276 AN XY: 74288

African (AFR) AF: 0.0572 AC: 2373 AN: 41462

American (AMR) AF: 0.202 AC: 3089 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3472

East Asian (EAS) AF: 0.0720 AC: 369 AN: 5126

South Asian (SAS) AF: 0.204 AC: 981 AN: 4808

European-Finnish (FIN) AF: 0.277 AC: 2925 AN: 10554

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16200 AN: 67956

Other (OTH) AF: 0.164 AC: 347 AN: 2112

Alfa AF: 0.208 Hom.: 5974

Bravo AF: 0.163

Asia WGS AF: 0.151 AC: 525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.90
DANN	Benign	0.79
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs17827152; hg19: chr4-55478686;