rs2338219

Variant names:

• chr5-72422251-C-T
• rs2338219

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 0.0792 in 152,192 control chromosomes in the GnomAD database, including 654 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 0.079 (654 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 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: 0.0792 AC: 12049 AN: 152074 Hom.: 653 Cov.: 33

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0721

Gnomad ASJ AF: 0.0436

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0533

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0806

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

GnomAD4 genome AF: 0.0792 AC: 12049 AN: 152192 Hom.: 654 Cov.: 33 AF XY: 0.0800 AC XY: 5949 AN XY: 74388

African (AFR) AF: 0.0200 AC: 833 AN: 41550

American (AMR) AF: 0.0720 AC: 1102 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0436 AC: 151 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0535 AC: 258 AN: 4822

European-Finnish (FIN) AF: 0.146 AC: 1544 AN: 10554

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7884 AN: 68008

Other (OTH) AF: 0.0793 AC: 167 AN: 2106

Alfa AF: 0.100 Hom.: 111

Bravo AF: 0.0704

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.37
DANN	Benign	0.36
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2338219; hg19: chr5-71718078; COSMIC: COSV72662116;