rs7303471

Variant names:

• chr12-33117978-T-C
• rs7303471

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.568 AC: 23516 AN: 41408

American (AMR) AF: 0.341 AC: 5208 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 973 AN: 3468

East Asian (EAS) AF: 0.810 AC: 4169 AN: 5148

South Asian (SAS) AF: 0.494 AC: 2376 AN: 4814

European-Finnish (FIN) AF: 0.206 AC: 2181 AN: 10584

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14179 AN: 67980

Other (OTH) AF: 0.326 AC: 688 AN: 2112

Alfa AF: 0.244 Hom.: 14342

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7303471; hg19: chr12-33270912;