chr12-73048715-C-T

Variant names:

• chr12-73048715-C-T
• rs1400142

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 0.644 in 151,374 control chromosomes in the GnomAD database, including 31,480 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 0.64 (31480 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.760
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.71 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: 0.644 AC: 97371 AN: 151256 Hom.: 31431 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.644 AC: 97482 AN: 151374 Hom.: 31480 Cov.: 32 AF XY: 0.646 AC XY: 47810 AN XY: 73976

African (AFR) AF: 0.625 AC: 25833 AN: 41358

American (AMR) AF: 0.607 AC: 9201 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2026 AN: 3458

East Asian (EAS) AF: 0.697 AC: 3562 AN: 5108

South Asian (SAS) AF: 0.730 AC: 3519 AN: 4820

European-Finnish (FIN) AF: 0.652 AC: 6880 AN: 10550

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.656 AC: 44323 AN: 67608

Other (OTH) AF: 0.622 AC: 1310 AN: 2106

Alfa AF: 0.652 Hom.: 16693

Bravo AF: 0.630

Asia WGS AF: 0.718 AC: 2495 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.0
DANN	Benign	0.36
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs1400142; hg19: chr12-73442495;