chr12-28002147-A-G

Variant names:

• chr12-28002147-A-G
• rs10771399

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 0.0915 in 152,168 control chromosomes in the GnomAD database, including 744 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 0.091 (744 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354
• Publications: 87 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0915 AC: 13911 AN: 152052 Hom.: 741 Cov.: 31

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0703

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.0915 AC: 13923 AN: 152168 Hom.: 744 Cov.: 31 AF XY: 0.0902 AC XY: 6708 AN XY: 74372

African (AFR) AF: 0.0387 AC: 1607 AN: 41554

American (AMR) AF: 0.0849 AC: 1297 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3468

East Asian (EAS) AF: 0.191 AC: 985 AN: 5168

South Asian (SAS) AF: 0.140 AC: 672 AN: 4814

European-Finnish (FIN) AF: 0.0703 AC: 744 AN: 10588

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7909 AN: 67992

Other (OTH) AF: 0.0882 AC: 186 AN: 2108

Alfa AF: 0.109 Hom.: 1964

Bravo AF: 0.0911

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.77
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs10771399; hg19: chr12-28155080;