12-38045401-C-T

Variant names:

• chr12-38045401-C-T
• rs2204008

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 0.298 in 151,548 control chromosomes in the GnomAD database, including 7,428 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 (7428 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45074 AN: 151432 Hom.: 7417 Cov.: 30

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.298 AC: 45091 AN: 151548 Hom.: 7428 Cov.: 30 AF XY: 0.299 AC XY: 22156 AN XY: 74034

African (AFR) AF: 0.160 AC: 6610 AN: 41308

American (AMR) AF: 0.342 AC: 5197 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1019 AN: 3450

East Asian (EAS) AF: 0.165 AC: 841 AN: 5112

South Asian (SAS) AF: 0.301 AC: 1450 AN: 4818

European-Finnish (FIN) AF: 0.415 AC: 4366 AN: 10508

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24599 AN: 67874

Other (OTH) AF: 0.293 AC: 616 AN: 2100

Alfa AF: 0.318 Hom.: 11474

Bravo AF: 0.291

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.63
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs2204008; hg19: chr12-38439203;