12-63832582-C-G

Variant names:

• chr12-63832582-C-G
• rs7302672

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 0.273 in 152,106 control chromosomes in the GnomAD database, including 6,489 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 0.27 (6489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 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: 0.273 AC: 41417 AN: 151986 Hom.: 6453 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.273 AC: 41511 AN: 152106 Hom.: 6489 Cov.: 32 AF XY: 0.277 AC XY: 20614 AN XY: 74370

African (AFR) AF: 0.387 AC: 16061 AN: 41466

American (AMR) AF: 0.255 AC: 3905 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 810 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2720 AN: 5162

South Asian (SAS) AF: 0.313 AC: 1509 AN: 4822

European-Finnish (FIN) AF: 0.259 AC: 2738 AN: 10576

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.190 AC: 12922 AN: 68008

Other (OTH) AF: 0.252 AC: 533 AN: 2112

Alfa AF: 0.0902 Hom.: 130

Bravo AF: 0.276

Asia WGS AF: 0.419 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.82
DANN	Benign	0.28
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7302672; hg19: chr12-64226362;