Genetic Variant GAPDHP64:n.107C>G (chr1-116714729-G-C) – 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 ENST00000419696.1(GAPDHP64):n.107C>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 0.00000248 in 403,862 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: 0.0000025 ( 0 hom. )

Consequence

GAPDHP64
ENST00000419696.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.74

Variant links:

Genes affected

GAPDHP64 (HGNC:4158): (glyceraldehyde-3-phosphate dehydrogenase pseudogene 64)

GAPDHP64 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=-0.65).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAPDHP64		n.116714729G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAPDHP64	ENST00000419696.1 link	n.107C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000248

AC:

AN:

403862

Hom.:

Cov.:

AF XY:

0.00000436

AC XY:

AN XY:

229348

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

11668

American (AMR)

AF:

0.00

AC:

AN:

37380

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13152

East Asian (EAS)

AF:

0.00

AC:

AN:

16028

South Asian (SAS)

AF:

0.0000148

AC:

AN:

67596

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20556

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1434

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

216872

Other (OTH)

AF:

0.00

AC:

AN:

19176

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

136

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

0.30

DANN

Benign

0.30

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over