12-46978487-C-T

Variant names:

• chr12-46978487-C-T
• rs2711721

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 0.361 in 151,956 control chromosomes in the GnomAD database, including 12,289 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 0.36 (12289 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 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: 0.361 AC: 54807 AN: 151838 Hom.: 12247 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.361 AC: 54915 AN: 151956 Hom.: 12289 Cov.: 31 AF XY: 0.358 AC XY: 26553 AN XY: 74260

African (AFR) AF: 0.639 AC: 26455 AN: 41418

American (AMR) AF: 0.301 AC: 4587 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3468

East Asian (EAS) AF: 0.431 AC: 2218 AN: 5150

South Asian (SAS) AF: 0.346 AC: 1668 AN: 4816

European-Finnish (FIN) AF: 0.184 AC: 1950 AN: 10570

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15922 AN: 67964

Other (OTH) AF: 0.351 AC: 740 AN: 2110

Alfa AF: 0.283 Hom.: 21786

Bravo AF: 0.384

Asia WGS AF: 0.394 AC: 1370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.45
DANN	Benign	0.21
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2711721; hg19: chr12-47372270; COSMIC: COSV50192731;