rs2243238

Variant names:

• chr5-132671728-C-T
• rs2243238

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 0.0926 in 151,818 control chromosomes in the GnomAD database, including 1,082 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 0.093 (1082 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14019 AN: 151698 Hom.: 1078 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0983

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0120

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.0867

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

GnomAD4 genome AF: 0.0926 AC: 14059 AN: 151818 Hom.: 1082 Cov.: 31 AF XY: 0.0921 AC XY: 6837 AN XY: 74202

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0984

Gnomad4 ASJ AF: 0.0648

Gnomad4 EAS AF: 0.0703

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0120

Gnomad4 NFE AF: 0.0385

Gnomad4 OTH AF: 0.0872

Alfa AF: 0.0663 Hom.: 77

Bravo AF: 0.104

Asia WGS AF: 0.105 AC: 366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.049
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243238; hg19: chr5-132007420;