chr12-56661507-C-T

Variant names:

• chr12-56661507-C-T
• rs2950390

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 43 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.262 AC: 10842 AN: 41450

American (AMR) AF: 0.269 AC: 4102 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1326 AN: 5182

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4820

European-Finnish (FIN) AF: 0.261 AC: 2757 AN: 10554

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23213 AN: 67958

Other (OTH) AF: 0.297 AC: 626 AN: 2106

Alfa AF: 0.324 Hom.: 36736

Bravo AF: 0.300

Asia WGS AF: 0.223 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.4
DANN	Benign	0.75
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2950390; hg19: chr12-57055291;