rs632973

Variant names:

• chr12-52533304-T-C
• rs632973

Your query was ambiguous. Multiple possible variants found:

• chr12-52533304-T-C
• chr12-52533304-T-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 0.528 in 151,974 control chromosomes in the GnomAD database, including 22,975 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 0.53 (22975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 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: 0.529 AC: 80278 AN: 151856 Hom.: 22978 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.528 AC: 80294 AN: 151974 Hom.: 22975 Cov.: 32 AF XY: 0.521 AC XY: 38679 AN XY: 74258

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.548

Alfa AF: 0.585 Hom.: 3433

Bravo AF: 0.516

Asia WGS AF: 0.392 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs632973; hg19: chr12-52927088;