rs7308752

Positions:

• chr12-91133404-A-G

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 0.247 in 151,930 control chromosomes in the GnomAD database, including 8,271 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 0.25 (8271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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 (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.247 AC: 37444 AN: 151812 Hom.: 8239 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0702

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0916

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.247 AC: 37530 AN: 151930 Hom.: 8271 Cov.: 32 AF XY: 0.243 AC XY: 18068 AN XY: 74246

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0702

Gnomad4 NFE AF: 0.0916

Gnomad4 OTH AF: 0.211

Alfa AF: 0.130 Hom.: 2193

Bravo AF: 0.274

Asia WGS AF: 0.247 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7308752; hg19: chr12-91527181;