12-10614592-T-C

Variant names:

• chr12-10614592-T-C
• rs6488313

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 0.762 in 152,130 control chromosomes in the GnomAD database, including 44,822 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 0.76 (44822 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.762 AC: 115899 AN: 152012 Hom.: 44787 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.762 AC: 115988 AN: 152130 Hom.: 44822 Cov.: 32 AF XY: 0.764 AC XY: 56812 AN XY: 74364

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.777

Alfa AF: 0.774 Hom.: 5687

Bravo AF: 0.760

Asia WGS AF: 0.906 AC: 3150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6488313; hg19: chr12-10767191;