rs4715384

Variant names:

• chr6-53215539-A-G
• rs4715384

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 0.15 in 152,210 control chromosomes in the GnomAD database, including 2,367 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 0.15 (2367 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 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: 0.150 AC: 22796 AN: 152092 Hom.: 2365 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0656

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.150 AC: 22812 AN: 152210 Hom.: 2367 Cov.: 33 AF XY: 0.149 AC XY: 11105 AN XY: 74414

African (AFR) AF: 0.289 AC: 11984 AN: 41516

American (AMR) AF: 0.157 AC: 2393 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 390 AN: 3466

East Asian (EAS) AF: 0.120 AC: 623 AN: 5182

South Asian (SAS) AF: 0.129 AC: 624 AN: 4824

European-Finnish (FIN) AF: 0.0656 AC: 695 AN: 10596

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0836 AC: 5686 AN: 68020

Other (OTH) AF: 0.149 AC: 315 AN: 2112

Alfa AF: 0.107 Hom.: 1833

Bravo AF: 0.164

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.4
DANN	Benign	0.72
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs4715384; hg19: chr6-53080337;