rs249851

Positions:

• chr12-98471193-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 0.209 in 151,896 control chromosomes in the GnomAD database, including 3,555 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 0.21 (3555 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 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: 0.209 AC: 31727 AN: 151778 Hom.: 3554 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0783

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.209 AC: 31742 AN: 151896 Hom.: 3555 Cov.: 31 AF XY: 0.205 AC XY: 15213 AN XY: 74232

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.0787

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.207

Alfa AF: 0.202 Hom.: 1598

Bravo AF: 0.215

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs249851; hg19: chr12-98864971;