chr12-8613765-C-G

Variant names:

• chr12-8613765-C-G
• rs714629

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 0.497 in 152,134 control chromosomes in the GnomAD database, including 19,480 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 0.50 (19480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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: 0.497 AC: 75541 AN: 152016 Hom.: 19483 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.497 AC: 75547 AN: 152134 Hom.: 19480 Cov.: 33 AF XY: 0.489 AC XY: 36348 AN XY: 74364

African (AFR) AF: 0.594 AC: 24637 AN: 41502

American (AMR) AF: 0.480 AC: 7346 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2207 AN: 3470

East Asian (EAS) AF: 0.161 AC: 834 AN: 5172

South Asian (SAS) AF: 0.429 AC: 2070 AN: 4828

European-Finnish (FIN) AF: 0.405 AC: 4282 AN: 10566

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32636 AN: 67982

Other (OTH) AF: 0.501 AC: 1058 AN: 2112

Alfa AF: 0.479 Hom.: 2267

Bravo AF: 0.509

Asia WGS AF: 0.328 AC: 1142 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	2.1
DANN	Benign	0.33
PhyloP100		0.094

Splicing

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

Other links and lift over

dbSNP: rs714629; hg19: chr12-8766361;