rs7303471

chr12-33117978-T-C

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 0.353 in 151,980 control chromosomes in the GnomAD database, including 12,013 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 0.35 (12013 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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 (EAS) allele frequency at 95% confidence interval = 0.789 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: 0.352 AC: 53517 AN: 151862 Hom.: 12008 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.353 AC: 53579 AN: 151980 Hom.: 12013 Cov.: 32 AF XY: 0.357 AC XY: 26483 AN XY: 74262

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.326

Alfa AF: 0.240 Hom.: 10165

Bravo AF: 0.375

Asia WGS AF: 0.636 AC: 2209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.13
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7303471; hg19: chr12-33270912;