rs997269

Positions:

• chr12-128153529-G-A

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 0.431 in 151,912 control chromosomes in the GnomAD database, including 14,321 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 0.43 (14321 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65486 AN: 151794 Hom.: 14313 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.431 AC: 65541 AN: 151912 Hom.: 14321 Cov.: 32 AF XY: 0.438 AC XY: 32528 AN XY: 74236

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.445

Alfa AF: 0.437 Hom.: 6821

Bravo AF: 0.425

Asia WGS AF: 0.499 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs997269; hg19: chr12-128638074;