Variant 7-128400645-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000883.4(IMPDH1):c.580-106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 1,265,432 control chromosomes in the GnomAD database, including 84,562 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 0.38 ( 10997 hom., cov: 33)

Exomes 𝑓: 0.36 ( 73565 hom. )

Consequence

IMPDH1
NM_000883.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.555

Variant links:

Genes affected

IMPDH1 (HGNC:6052): (inosine monophosphate dehydrogenase 1) The protein encoded by this gene acts as a homotetramer to regulate cell growth. The encoded protein is an enzyme that catalyzes the synthesis of xanthine monophosphate (XMP) from inosine-5'-monophosphate (IMP). This is the rate-limiting step in the de novo synthesis of guanine nucleotides. Defects in this gene are a cause of retinitis pigmentosa type 10 (RP10). Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

IMPDH1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IMPDH1	NM_000883.4 link	c.580-106G>A		intron_variant		ENST00000338791.11	NP_000874.2	P20839-6B3KRZ3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IMPDH1	ENST00000338791.11 link	c.580-106G>A		intron_variant		2	NM_000883.4	ENSP00000345096.6		P20839-6

Frequencies

GnomAD3 genomes

AF:

0.378

AC:

57376

AN:

151962

Hom.:

10997

Cov.:

show subpopulations

Gnomad AFR

AF:

0.406

Gnomad AMI

AF:

0.267

Gnomad AMR

AF:

0.379

Gnomad ASJ

AF:

0.432

Gnomad EAS

AF:

0.545

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.374

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.365

GnomAD4 exome

AF:

0.360

AC:

400663

AN:

1113352

Hom.:

73565

Cov.:

AF XY:

0.362

AC XY:

205092

AN XY:

566678

show subpopulations

Gnomad4 AFR exome

AF:

0.402

Gnomad4 AMR exome

AF:

0.407

Gnomad4 ASJ exome

AF:

0.428

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.416

Gnomad4 FIN exome

AF:

0.379

Gnomad4 NFE exome

AF:

0.341

Gnomad4 OTH exome

AF:

0.368

GnomAD4 genome

AF:

0.378

AC:

57415

AN:

152080

Hom.:

10997

Cov.:

AF XY:

0.381

AC XY:

28312

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.406

Gnomad4 AMR

AF:

0.380

Gnomad4 ASJ

AF:

0.432

Gnomad4 EAS

AF:

0.545

Gnomad4 SAS

AF:

0.428

Gnomad4 FIN

AF:

0.374

Gnomad4 NFE

AF:

0.343

Gnomad4 OTH

AF:

0.368

Alfa

AF:

0.352

Hom.:

10120

Bravo

AF:

0.380

Asia WGS

AF:

0.474

AC:

1651

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.3

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over