12-28008815-T-C

Variant names:

• chr12-28008815-T-C
• rs1975930

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 0.0887 in 143,326 control chromosomes in the GnomAD database, including 675 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 0.089 (675 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 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: 0.0888 AC: 12718 AN: 143190 Hom.: 675 Cov.: 31

Gnomad AFR AF: 0.0228

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.0949

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0819

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.0777

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

GnomAD4 genome AF: 0.0887 AC: 12718 AN: 143326 Hom.: 675 Cov.: 31 AF XY: 0.0873 AC XY: 6081 AN XY: 69618

African (AFR) AF: 0.0228 AC: 894 AN: 39172

American (AMR) AF: 0.0802 AC: 1166 AN: 14532

Ashkenazi Jewish (ASJ) AF: 0.0949 AC: 319 AN: 3362

East Asian (EAS) AF: 0.222 AC: 989 AN: 4450

South Asian (SAS) AF: 0.148 AC: 610 AN: 4118

European-Finnish (FIN) AF: 0.0819 AC: 737 AN: 8998

Middle Eastern (MID) AF: 0.108 AC: 31 AN: 288

European-Non Finnish (NFE) AF: 0.118 AC: 7702 AN: 65498

Other (OTH) AF: 0.0775 AC: 158 AN: 2040

Alfa AF: 0.106 Hom.: 434

Bravo AF: 0.0825

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.44
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1975930; hg19: chr12-28161748;