12-21128955-T-G

Position:

• chr12-21128955-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.884 in 151,922 control chromosomes in the GnomAD database, including 59,939 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 0.88 (59939 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134177 AN: 151804 Hom.: 59894 Cov.: 29

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.943

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.884 AC: 134280 AN: 151922 Hom.: 59939 Cov.: 29 AF XY: 0.884 AC XY: 65684 AN XY: 74262

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.943

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.899

Alfa AF: 0.933 Hom.: 86935

Bravo AF: 0.880

Asia WGS AF: 0.928 AC: 3225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs852549; hg19: chr12-21281889;