rs1863552

Positions:

• chr12-108065498-G-A
• chr12-108065498-G-T

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 0.0242 in 152,276 control chromosomes in the GnomAD database, including 82 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 0.024 (82 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0792 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: 0.0242 AC: 3681 AN: 152160 Hom.: 82 Cov.: 32

Gnomad AFR AF: 0.0422

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0128

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.0703

Gnomad SAS AF: 0.0868

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0113

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0242 AC: 3683 AN: 152276 Hom.: 82 Cov.: 32 AF XY: 0.0250 AC XY: 1858 AN XY: 74448

Gnomad4 AFR AF: 0.0421

Gnomad4 AMR AF: 0.0131

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.0705

Gnomad4 SAS AF: 0.0860

Gnomad4 FIN AF: 0.00339

Gnomad4 NFE AF: 0.0113

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.0149 Hom.: 47

Bravo AF: 0.0244

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1863552; hg19: chr12-108459275;