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
• Publications: 3 publications found

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419696.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAPDHP64	ENST00000419696.1	TSL:6	n.107C>A		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.28
DANN	Benign	0.44
PhyloP100		2.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4271251;

hg19: chr1-117257351;