chr12-53417250-T-C

Variant names:

• chr12-53417250-T-C
• rs10876450

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 0.174 in 152,046 control chromosomes in the GnomAD database, including 2,361 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 0.17 (2361 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 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: 0.174 AC: 26408 AN: 151930 Hom.: 2356 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.174 AC: 26429 AN: 152046 Hom.: 2361 Cov.: 31 AF XY: 0.174 AC XY: 12913 AN XY: 74306

African (AFR) AF: 0.180 AC: 7473 AN: 41466

American (AMR) AF: 0.200 AC: 3050 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3466

East Asian (EAS) AF: 0.175 AC: 907 AN: 5172

South Asian (SAS) AF: 0.145 AC: 699 AN: 4822

European-Finnish (FIN) AF: 0.159 AC: 1676 AN: 10564

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11730 AN: 67976

Other (OTH) AF: 0.148 AC: 312 AN: 2106

Alfa AF: 0.168 Hom.: 2844

Bravo AF: 0.174

Asia WGS AF: 0.146 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.54
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs10876450; hg19: chr12-53811034;