3-160751268-T-C

Variant names:

• chr3-160751268-T-C
• rs959960
• NR_185913.1:n.4184A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_185913.1(PPM1L-DT):​n.4184A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 151,930 control chromosomes in the GnomAD database, including 25,797 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 0.55 (25797 hom., cov: 31)
• Consequence: PPM1L-DT NR_185913.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 4 publications found

Genes affected

PPM1L-DT (HGNC:55390): (PPM1L divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_185913.1. 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
	PPM1L-DT	NR_185913.1		n.4184A>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPM1L-DT	ENST00000748637.1		n.636+3248A>G		intron	N/A
	PPM1L-DT	ENST00000748638.1		n.558+3326A>G		intron	N/A
	PPM1L-DT	ENST00000748639.1		n.543+3334A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82848 AN: 151812 Hom.: 25741 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.546 AC: 82963 AN: 151930 Hom.: 25797 Cov.: 31 AF XY: 0.541 AC XY: 40205 AN XY: 74260

African (AFR) AF: 0.860 AC: 35632 AN: 41432

American (AMR) AF: 0.529 AC: 8078 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1278 AN: 3468

East Asian (EAS) AF: 0.669 AC: 3454 AN: 5162

South Asian (SAS) AF: 0.432 AC: 2075 AN: 4800

European-Finnish (FIN) AF: 0.332 AC: 3507 AN: 10550

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27366 AN: 67942

Other (OTH) AF: 0.497 AC: 1043 AN: 2098

Alfa AF: 0.460 Hom.: 37277

Bravo AF: 0.575

Asia WGS AF: 0.567 AC: 1966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs959960; hg19: chr3-160469056;