1-116714729-G-T

Variant names:

• chr1-116714729-G-T
• rs4271251
• ENST00000419696.1:n.107C>A

Variant summary

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

The ENST00000419696.1(GAPDHP64):​n.107C>A 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 0.183 in 555,626 control chromosomes in the GnomAD database, including 10,021 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 0.17 (2355 hom., cov: 32)
  • Exomes 𝑓: 0.19 (7666 hom.)
• Consequence: GAPDHP64 ENST00000419696.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.74

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25610 AN: 151966 Hom.: 2350 Cov.: 32

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0447

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.179

GnomAD4 exome AF: 0.189 AC: 76303 AN: 403542 Hom.: 7666 Cov.: 0 AF XY: 0.191 AC XY: 43677 AN XY: 229130

African (AFR) AF: 0.0944 AC: 1101 AN: 11660

American (AMR) AF: 0.163 AC: 6103 AN: 37354

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 1961 AN: 13128

East Asian (EAS) AF: 0.0381 AC: 611 AN: 16024

South Asian (SAS) AF: 0.188 AC: 12716 AN: 67572

European-Finnish (FIN) AF: 0.242 AC: 4967 AN: 20520

Middle Eastern (MID) AF: 0.177 AC: 253 AN: 1428

European-Non Finnish (NFE) AF: 0.208 AC: 44985 AN: 216696

Other (OTH) AF: 0.188 AC: 3606 AN: 19160

GnomAD4 genome AF: 0.168 AC: 25626 AN: 152084 Hom.: 2355 Cov.: 32 AF XY: 0.170 AC XY: 12614 AN XY: 74354

African (AFR) AF: 0.0983 AC: 4077 AN: 41496

American (AMR) AF: 0.170 AC: 2589 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3468

East Asian (EAS) AF: 0.0450 AC: 233 AN: 5180

South Asian (SAS) AF: 0.190 AC: 916 AN: 4824

European-Finnish (FIN) AF: 0.239 AC: 2523 AN: 10568

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14097 AN: 67958

Other (OTH) AF: 0.178 AC: 375 AN: 2112

Alfa AF: 0.0738 Hom.: 136

Bravo AF: 0.159

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.28
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4271251; hg19: chr1-117257351;