1-119435210-C-A

Variant names:

• chr1-119435210-C-A
• rs1417608
• ENST00000632456.2:n.769-63G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000632456.2(ENSG00000293080):​n.769-63G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000814 in 208,938 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: 𝑓 0.000092 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000053 (0 hom.)
• Consequence: ENSG00000293080 ENST00000632456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 3 publications found

Genes affected

ENSG00000293080 (HGNC:):

GAPDHP74 (HGNC:50647): (glyceraldehyde-3-phosphate dehydrogenase pseudogene 74)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293080	ENST00000632456.2	n.769-63G>T		intron_variant	Intron 6 of 6	6
ENSG00000293080	ENST00000756944.1	n.340-63G>T		intron_variant	Intron 3 of 3
ENSG00000293080	ENST00000756945.1	n.519-63G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0000920 AC: 14 AN: 152106 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000191

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000528 AC: 3 AN: 56832 Hom.: 0 AF XY: 0.0000672 AC XY: 2 AN XY: 29780

African (AFR) AF: 0.00 AC: 0 AN: 838

American (AMR) AF: 0.00 AC: 0 AN: 1928

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1326

East Asian (EAS) AF: 0.00 AC: 0 AN: 1402

South Asian (SAS) AF: 0.00 AC: 0 AN: 7834

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2862

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 286

European-Non Finnish (NFE) AF: 0.0000816 AC: 3 AN: 36780

Other (OTH) AF: 0.00 AC: 0 AN: 3576

GnomAD4 genome AF: 0.0000920 AC: 14 AN: 152106 Hom.: 0 Cov.: 33 AF XY: 0.0000808 AC XY: 6 AN XY: 74300

African (AFR) AF: 0.00 AC: 0 AN: 41380

American (AMR) AF: 0.0000654 AC: 1 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.000191 AC: 13 AN: 68022

Other (OTH) AF: 0.00 AC: 0 AN: 2090

Alfa AF: 0.00 Hom.: 91

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.37
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1417608; hg19: chr1-119977833;