rs1891269

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-91667068-A-C
• chr10-91667068-A-G
• chr10-91667068-A-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAPDHP28		n.91667068A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAPDHP28	ENST00000455134.1	n.715T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs1891269; hg19: chr10-93426825;