rs7294500

Variant names:

• chr12-33272747-G-A
• rs7294500

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;