1-45628020-G-C

Variant names:

• chr1-45628020-G-C
• rs1135850
• NM_021639.5:c.*236C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_021639.5(GPBP1L1):​c.*236C>G variant causes a 3 prime UTR 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: GPBP1L1 NM_021639.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 13 publications found

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]

ACMG classification

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=-0.91).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 313390 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 166448

African (AFR) AF: 0.00 AC: 0 AN: 9320

American (AMR) AF: 0.00 AC: 0 AN: 13862

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9454

East Asian (EAS) AF: 0.00 AC: 0 AN: 19394

South Asian (SAS) AF: 0.00 AC: 0 AN: 39726

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 17040

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1342

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 185378

Other (OTH) AF: 0.00 AC: 0 AN: 17874

GnomAD4 genome Cov.: 32

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	-0.91
CADD	Benign	2.6
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

Other links and lift over

dbSNP: rs1135850; hg19: chr1-46093692;