rs12261589

Variant names:

• chr10-77781077-C-T
• rs12261589
• ENST00000439688.1:n.800G>A

Variant summary

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

The ENST00000439688.1(IMPDH1P5):​n.800G>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 0.0101 in 885,354 control chromosomes in the GnomAD database, including 550 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 0.038 (367 hom., cov: 32)
  • Exomes 𝑓: 0.0044 (183 hom.)
• Consequence: IMPDH1P5 ENST00000439688.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 3 publications found

Genes affected

IMPDH1P5 (HGNC:33960): (inosine monophosphate dehydrogenase 1 pseudogene 5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439688.1. 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
	IMPDH1P5	ENST00000439688.1	TSL:6	n.800G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0376 AC: 5715 AN: 152126 Hom.: 366 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0144

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000397

Gnomad OTH AF: 0.0249

GnomAD4 exome AF: 0.00444 AC: 3258 AN: 733110 Hom.: 183 Cov.: 9 AF XY: 0.00359 AC XY: 1403 AN XY: 391042

African (AFR) AF: 0.128 AC: 2514 AN: 19612

American (AMR) AF: 0.00612 AC: 264 AN: 43156

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20258

East Asian (EAS) AF: 0.00 AC: 0 AN: 36334

South Asian (SAS) AF: 0.000357 AC: 25 AN: 70004

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49468

Middle Eastern (MID) AF: 0.00294 AC: 10 AN: 3396

European-Non Finnish (NFE) AF: 0.000270 AC: 123 AN: 455114

Other (OTH) AF: 0.00900 AC: 322 AN: 35768

GnomAD4 genome AF: 0.0376 AC: 5724 AN: 152244 Hom.: 367 Cov.: 32 AF XY: 0.0362 AC XY: 2697 AN XY: 74442

African (AFR) AF: 0.131 AC: 5423 AN: 41522

American (AMR) AF: 0.0143 AC: 219 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10612

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000397 AC: 27 AN: 68024

Other (OTH) AF: 0.0246 AC: 52 AN: 2114

Alfa AF: 0.0238 Hom.: 329

Bravo AF: 0.0422

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.32
DANN	Benign	0.51
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs12261589; hg19: chr10-79540835;