chr12-18873148-G-C

Variant names:

• chr12-18873148-G-C
• rs726391

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 0.584 in 151,994 control chromosomes in the GnomAD database, including 31,034 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 0.58 (31034 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.781 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: 0.584 AC: 88701 AN: 151876 Hom.: 31038 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.584 AC: 88700 AN: 151994 Hom.: 31034 Cov.: 32 AF XY: 0.583 AC XY: 43278 AN XY: 74286

African (AFR) AF: 0.186 AC: 7700 AN: 41462

American (AMR) AF: 0.575 AC: 8766 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2279 AN: 3468

East Asian (EAS) AF: 0.473 AC: 2429 AN: 5140

South Asian (SAS) AF: 0.749 AC: 3608 AN: 4820

European-Finnish (FIN) AF: 0.789 AC: 8344 AN: 10570

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.787 AC: 53506 AN: 67980

Other (OTH) AF: 0.609 AC: 1288 AN: 2114

Alfa AF: 0.596 Hom.: 2488

Bravo AF: 0.546

Asia WGS AF: 0.594 AC: 2065 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.77
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs726391; hg19: chr12-19026082;