rs2243294

Variant names:

• chr5-132684123-G-A
• rs2243294

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 0.568 in 151,980 control chromosomes in the GnomAD database, including 27,400 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 0.57 (27400 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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 = 0.734 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: 0.568 AC: 86243 AN: 151862 Hom.: 27403 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.568 AC: 86254 AN: 151980 Hom.: 27400 Cov.: 31 AF XY: 0.558 AC XY: 41483 AN XY: 74296

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.595

Alfa AF: 0.636 Hom.: 4031

Bravo AF: 0.550

Asia WGS AF: 0.440 AC: 1532 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	1.6
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243294; hg19: chr5-132019815; COSMIC: COSV51502846;