rs4271251

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-116714729-G-A
• chr1-116714729-G-C
• chr1-116714729-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000419696.1(GAPDHP64):​n.107C>T 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 0.00000743 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: 0.0000074 (0 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: 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=-0.63).

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>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000743 AC: 3 AN: 403862 Hom.: 0 Cov.: 0 AF XY: 0.00000872 AC XY: 2 AN XY: 229348

African (AFR) AF: 0.00 AC: 0 AN: 11668

American (AMR) AF: 0.00 AC: 0 AN: 37380

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13152

East Asian (EAS) AF: 0.0000624 AC: 1 AN: 16028

South Asian (SAS) AF: 0.0000148 AC: 1 AN: 67596

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1434

European-Non Finnish (NFE) AF: 0.00000461 AC: 1 AN: 216872

Other (OTH) AF: 0.00 AC: 0 AN: 19176

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 136

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	0.37
DANN	Benign	0.62
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;