rs2243294

Positions:

• chr5-132684123-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;