rs1863552

Variant names:

• chr12-108065498-G-A
• rs1863552

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0421 AC: 1750 AN: 41546

American (AMR) AF: 0.0131 AC: 200 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3472

East Asian (EAS) AF: 0.0705 AC: 365 AN: 5178

South Asian (SAS) AF: 0.0860 AC: 415 AN: 4824

European-Finnish (FIN) AF: 0.00339 AC: 36 AN: 10612

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.0113 AC: 771 AN: 68028

Other (OTH) AF: 0.0241 AC: 51 AN: 2114

Alfa AF: 0.0156 Hom.: 55

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1863552; hg19: chr12-108459275;