rs2243238

Positions:

• chr5-132671728-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 0.0926 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/exons	MANE	UniProt

Ensembl

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