chr12-65140844-C-A

Variant names:

• chr12-65140844-C-A
• rs6581612

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 0.732 in 151,998 control chromosomes in the GnomAD database, including 40,968 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 0.73 (40968 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.732 AC: 111190 AN: 151880 Hom.: 40936 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.732 AC: 111269 AN: 151998 Hom.: 40968 Cov.: 31 AF XY: 0.739 AC XY: 54913 AN XY: 74296

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.767

Alfa AF: 0.754 Hom.: 88861

Bravo AF: 0.725

Asia WGS AF: 0.915 AC: 3177 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.15
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6581612; hg19: chr12-65534624;