rs7294500

chr12-33272747-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 0.0819 in 151,550 control chromosomes in the GnomAD database, including 954 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 0.082 (954 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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: 0.0819 AC: 12398 AN: 151432 Hom.: 953 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.0425

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0310

Gnomad OTH AF: 0.0724

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

GnomAD4 genome AF: 0.0819 AC: 12405 AN: 151550 Hom.: 954 Cov.: 31 AF XY: 0.0802 AC XY: 5939 AN XY: 74092

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0509

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0429

Gnomad4 FIN AF: 0.0425

Gnomad4 NFE AF: 0.0310

Gnomad4 OTH AF: 0.0716

Alfa AF: 0.0396 Hom.: 357

Bravo AF: 0.0889

Asia WGS AF: 0.0250 AC: 88 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.2
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: rs7294500; hg19: chr12-33425682;