rs714629

Positions:

• chr12-8613765-C-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 0.497 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.501

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714629; hg19: chr12-8766361;