chr10-91667068-A-C

Variant names:

• chr10-91667068-A-C
• rs1891269
• ENST00000455134.1:n.715T>G

Variant summary

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

The ENST00000455134.1(GAPDHP28):​n.715T>G 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 0.727 in 382,494 control chromosomes in the GnomAD database, including 103,340 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 0.74 (42331 hom., cov: 32)
  • Exomes 𝑓: 0.72 (61009 hom.)
• Consequence: GAPDHP28 ENST00000455134.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.84
• Publications: 1 publications found

Genes affected

GAPDHP28 (HGNC:37780): (glyceraldehyde 3 phosphate dehydrogenase pseudogene 28)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455134.1. 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
	GAPDHP28	ENST00000455134.1	TSL:6	n.715T>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.739 AC: 111989 AN: 151532 Hom.: 42284 Cov.: 32

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.690

GnomAD4 exome AF: 0.719 AC: 165997 AN: 230840 Hom.: 61009 Cov.: 0 AF XY: 0.731 AC XY: 93084 AN XY: 127394

African (AFR) AF: 0.862 AC: 5235 AN: 6072

American (AMR) AF: 0.801 AC: 11667 AN: 14572

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 3660 AN: 5230

East Asian (EAS) AF: 0.925 AC: 8735 AN: 9442

South Asian (SAS) AF: 0.830 AC: 36378 AN: 43822

European-Finnish (FIN) AF: 0.815 AC: 12336 AN: 15134

Middle Eastern (MID) AF: 0.632 AC: 479 AN: 758

European-Non Finnish (NFE) AF: 0.639 AC: 79822 AN: 124842

Other (OTH) AF: 0.701 AC: 7685 AN: 10968

GnomAD4 genome AF: 0.739 AC: 112097 AN: 151654 Hom.: 42331 Cov.: 32 AF XY: 0.752 AC XY: 55673 AN XY: 74076

African (AFR) AF: 0.855 AC: 35401 AN: 41386

American (AMR) AF: 0.742 AC: 11303 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2385 AN: 3470

East Asian (EAS) AF: 0.920 AC: 4712 AN: 5122

South Asian (SAS) AF: 0.851 AC: 4094 AN: 4812

European-Finnish (FIN) AF: 0.819 AC: 8588 AN: 10492

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43445 AN: 67830

Other (OTH) AF: 0.688 AC: 1447 AN: 2104

Alfa AF: 0.608 Hom.: 1772

Bravo AF: 0.735

Asia WGS AF: 0.883 AC: 3071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.78
DANN	Benign	0.56
PhyloP100		2.8

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: rs1891269;

hg19: chr10-93426825;