rs1388090

Variant names:

• chr12-18859529-T-C
• rs1388090

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 0.873 in 151,950 control chromosomes in the GnomAD database, including 58,052 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 0.87 (58052 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 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: 0.873 AC: 132502 AN: 151832 Hom.: 58026 Cov.: 31

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.873 AC: 132579 AN: 151950 Hom.: 58052 Cov.: 31 AF XY: 0.873 AC XY: 64784 AN XY: 74236

African (AFR) AF: 0.802 AC: 33244 AN: 41460

American (AMR) AF: 0.912 AC: 13902 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3027 AN: 3464

East Asian (EAS) AF: 0.983 AC: 5035 AN: 5122

South Asian (SAS) AF: 0.878 AC: 4229 AN: 4816

European-Finnish (FIN) AF: 0.889 AC: 9402 AN: 10576

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60804 AN: 67948

Other (OTH) AF: 0.882 AC: 1867 AN: 2116

Alfa AF: 0.891 Hom.: 99042

Bravo AF: 0.873

Asia WGS AF: 0.927 AC: 3225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.81
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1388090; hg19: chr12-19012463;