rs1800799

Variant names:

• chr12-14886361-G-A
• rs1800799
• ENST00000527783.1:n.76-12808G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-14886361-G-A
• chr12-14886361-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000527783.1(C12orf60):​n.76-12808G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0298 in 152,266 control chromosomes in the GnomAD database, including 89 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 0.030 (89 hom., cov: 32)
• Consequence: C12orf60 ENST00000527783.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

Genes affected

C12orf60 (HGNC:28726): (chromosome 12 open reading frame 60)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0298 (4533/152266) while in subpopulation NFE AF= 0.0452 (3074/68018). AF 95% confidence interval is 0.0439. There are 89 homozygotes in gnomad4. There are 2168 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 89 AR gene

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
C12orf60	ENST00000527783.1	n.76-12808G>A		intron_variant	Intron 1 of 3	2
C12orf60	ENST00000533472.1	n.87-17646G>A		intron_variant	Intron 1 of 1	3
C12orf60	ENST00000543822.1	n.91+555G>A		intron_variant	Intron 1 of 1	3
C12orf60	ENST00000648334.1	n.126-17646G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0298 AC: 4533 AN: 152148 Hom.: 89 Cov.: 32

Gnomad AFR AF: 0.00830

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0188

Gnomad ASJ AF: 0.0409

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00642

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0298 AC: 4533 AN: 152266 Hom.: 89 Cov.: 32 AF XY: 0.0291 AC XY: 2168 AN XY: 74440

Gnomad4 AFR AF: 0.00828

Gnomad4 AMR AF: 0.0188

Gnomad4 ASJ AF: 0.0409

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00663

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.0452

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0196 Hom.: 9

Bravo AF: 0.0264

Asia WGS AF: 0.00433 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800799; hg19: chr12-15039295;