ENST00000632456.2:n.769-63G>A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000632456.2(ENSG00000293080):​n.769-63G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 208,918 control chromosomes in the GnomAD database, including 2,359 homozygotes. 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 0.14 (2133 hom., cov: 33)
  • Exomes 𝑓: 0.077 (226 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

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>A		intron_variant	Intron 6 of 6	6
ENSG00000293080	ENST00000756944.1	n.340-63G>A		intron_variant	Intron 3 of 3
ENSG00000293080	ENST00000756945.1	n.519-63G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21297 AN: 152050 Hom.: 2129 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0679

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.0771 AC: 4373 AN: 56750 Hom.: 226 AF XY: 0.0781 AC XY: 2323 AN XY: 29732

African (AFR) AF: 0.255 AC: 212 AN: 832

American (AMR) AF: 0.122 AC: 235 AN: 1922

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 154 AN: 1326

East Asian (EAS) AF: 0.0558 AC: 78 AN: 1398

South Asian (SAS) AF: 0.0986 AC: 771 AN: 7822

European-Finnish (FIN) AF: 0.0346 AC: 99 AN: 2862

Middle Eastern (MID) AF: 0.154 AC: 44 AN: 286

European-Non Finnish (NFE) AF: 0.0685 AC: 2517 AN: 36728

Other (OTH) AF: 0.0736 AC: 263 AN: 3574

GnomAD4 genome AF: 0.140 AC: 21327 AN: 152168 Hom.: 2133 Cov.: 33 AF XY: 0.139 AC XY: 10337 AN XY: 74410

African (AFR) AF: 0.277 AC: 11496 AN: 41474

American (AMR) AF: 0.148 AC: 2258 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3470

East Asian (EAS) AF: 0.0681 AC: 352 AN: 5172

South Asian (SAS) AF: 0.114 AC: 549 AN: 4824

European-Finnish (FIN) AF: 0.0322 AC: 342 AN: 10612

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0792 AC: 5383 AN: 68004

Other (OTH) AF: 0.145 AC: 305 AN: 2110

Alfa AF: 0.0518 Hom.: 91

Bravo AF: 0.155

Asia WGS AF: 0.106 AC: 372 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.45
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;