rs12692340

chr2-5296398-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 0.826 in 152,120 control chromosomes in the GnomAD database, including 55,092 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 0.83 (55092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.862

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 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: 0.826 AC: 125620 AN: 152002 Hom.: 55088 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.826 AC: 125658 AN: 152120 Hom.: 55092 Cov.: 32 AF XY: 0.832 AC XY: 61859 AN XY: 74374

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.912

Gnomad4 ASJ AF: 0.964

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.955

Gnomad4 OTH AF: 0.848

Alfa AF: 0.887 Hom.: 14077

Bravo AF: 0.805

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.14
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12692340; hg19: chr2-5436531;