rs60378296

Variant names:

• chr1-13223386-C-A
• rs60378296
• NM_001099850.2:c.1386G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-13223386-C-A
• chr1-13223386-C-T

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_001099850.2(PRAMEF18):​c.1386G>T​(p.Thr462Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T462T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00022 (2 hom., cov: 3)
  • Exomes 𝑓: 0.00015 (43 hom.)
  • Failed GnomAD Quality Control
• Consequence: PRAMEF18 NM_001099850.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.71
• Publications: 0 publications found

Genes affected

PRAMEF18 (HGNC:30693): (PRAME family member 18) Predicted to be involved in several processes, including negative regulation of apoptotic process; negative regulation of transcription, DNA-templated; and positive regulation of cell population proliferation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BP7: Synonymous conserved (PhyloP=-3.71 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099850.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRAMEF18	NM_001099850.2	MANE Select	c.1386G>T	p.Thr462Thr	synonymous	Exon 3 of 3	NP_001093320.2	Q5VWM3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRAMEF18	ENST00000624297.3	TSL:1 MANE Select	c.1386G>T	p.Thr462Thr	synonymous	Exon 3 of 3	ENSP00000485473.2	Q5VWM3

Frequencies

GnomAD3 genomes AF: 0.000224 AC: 8 AN: 35678 Hom.: 2 Cov.: 3

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000382

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00525

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000150 AC: 185 AN: 1234818 Hom.: 43 Cov.: 28 AF XY: 0.000225 AC XY: 138 AN XY: 614188

African (AFR) AF: 0.00 AC: 0 AN: 28000

American (AMR) AF: 0.000358 AC: 13 AN: 36304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19694

East Asian (EAS) AF: 0.0000450 AC: 1 AN: 22202

South Asian (SAS) AF: 0.00207 AC: 162 AN: 78144

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40604

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3244

European-Non Finnish (NFE) AF: 0.00000522 AC: 5 AN: 958710

Other (OTH) AF: 0.0000835 AC: 4 AN: 47916

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000224 AC: 8 AN: 35684 Hom.: 2 Cov.: 3 AF XY: 0.000238 AC XY: 4 AN XY: 16794

African (AFR) AF: 0.00 AC: 0 AN: 7264

American (AMR) AF: 0.000383 AC: 1 AN: 2612

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 824

East Asian (EAS) AF: 0.00 AC: 0 AN: 1192

South Asian (SAS) AF: 0.00522 AC: 7 AN: 1342

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1524

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 92

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 20236

Other (OTH) AF: 0.00 AC: 0 AN: 490

Alfa AF: 0.143 Hom.: 456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.5
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs60378296; hg19: chr1-13328887;