rs2338219

Positions:

• chr5-72422251-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.0200

Gnomad4 AMR AF: 0.0720

Gnomad4 ASJ AF: 0.0436

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0535

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0793

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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