12-94886937-T-C

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 0.502 in 151,886 control chromosomes in the GnomAD database, including 19,803 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 0.50 (19803 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 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: 0.502 AC: 76136 AN: 151768 Hom.: 19774 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.502 AC: 76198 AN: 151886 Hom.: 19803 Cov.: 31 AF XY: 0.505 AC XY: 37462 AN XY: 74246

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.509

Alfa AF: 0.426 Hom.: 17592

Bravo AF: 0.520

Asia WGS AF: 0.492 AC: 1694 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.4
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10777647; hg19: chr12-95280713;