12-56661507-C-T

Variant names:

• chr12-56661507-C-T
• rs2950390

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 0.299 in 152,012 control chromosomes in the GnomAD database, including 6,978 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 0.30 (6978 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 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: 0.299 AC: 45430 AN: 151894 Hom.: 6972 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.299 AC: 45473 AN: 152012 Hom.: 6978 Cov.: 31 AF XY: 0.294 AC XY: 21848 AN XY: 74296

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.297

Alfa AF: 0.326 Hom.: 18025

Bravo AF: 0.300

Asia WGS AF: 0.223 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2950390; hg19: chr12-57055291;