ENST00000375465.7:n.*169T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000375465.7(BPIFA4P):​n.170T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

BPIFA4P
ENST00000375465.7 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.357

Publications

0 publications found
Variant links:
Genes affected
BPIFA4P (HGNC:20469): (BPI fold containing family A member 4, pseudogene) Predicted to enable lipid binding activity. Predicted to be involved in regulation of liquid surface tension. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BPIFA4PNR_026760.1 linkn.170T>C non_coding_transcript_exon_variant Exon 3 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BPIFA4PENST00000375465.7 linkn.170T>C non_coding_transcript_exon_variant Exon 3 of 9 1
BPIFA4PENST00000420169.4 linkn.139T>C non_coding_transcript_exon_variant Exon 2 of 5 1
BPIFA4PENST00000603168.3 linkn.119T>C non_coding_transcript_exon_variant Exon 2 of 7 6

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1638
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
862
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
1536
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
72
Other (OTH)
AF:
0.00
AC:
0
AN:
22
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.9
DANN
Benign
0.59
PhyloP100
-0.36

Splicing

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

Publications

Other links and lift over

hg19: chr20-31787139; API