Genetic Variant GPBP1L1:c.*236C>A (chr1-45628020-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

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

The NM_021639.5(GPBP1L1):c.*236C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000957 in 313,390 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000096 ( 0 hom. )

Consequence

GPBP1L1
NM_021639.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0500

Publications

13 publications found

Variant links:

Genes affected

GPBP1L1 (HGNC:28843): (GC-rich promoter binding protein 1 like 1) Predicted to enable DNA binding activity and RNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

GPBP1L1 links:

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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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPBP1L1	NM_021639.5 link	c.*236C>A		3_prime_UTR_variant	Exon 13 of 13	ENST00000355105.8	NP_067652.1	Q9HC44

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPBP1L1	ENST00000355105.8 link	c.*236C>A		3_prime_UTR_variant	Exon 13 of 13	1	NM_021639.5	ENSP00000347224.3		Q9HC44

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000957

AC:

AN:

313390

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

166448

show subpopulations

African (AFR)

AF:

0.000107

AC:

AN:

9320

American (AMR)

AF:

0.00

AC:

AN:

13862

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9454

East Asian (EAS)

AF:

0.00

AC:

AN:

19394

South Asian (SAS)

AF:

0.00

AC:

AN:

39726

European-Finnish (FIN)

AF:

0.00

AC:

AN:

17040

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1342

European-Non Finnish (NFE)

AF:

0.0000108

AC:

AN:

185378

Other (OTH)

AF:

0.00

AC:

AN:

17874

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

2434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.5

(source)

DANN

Benign

0.38

PhyloP100

-0.050

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over