Variant chr7-128409519-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000883.4(IMPDH1):c.147-35G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0395 in 1,611,944 control chromosomes in the GnomAD database, including 2,478 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.049 ( 338 hom., cov: 33)

Exomes 𝑓: 0.039 ( 2140 hom. )

Consequence

IMPDH1
NM_000883.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0750

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP6

Variant 7-128409519-C-T is Benign according to our data. Variant chr7-128409519-C-T is described in ClinVar as [Benign]. Clinvar id is 1181857.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMPDH1	NM_000883.4 linkuse as main transcript	c.147-35G>A		intron_variant		ENST00000338791.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMPDH1	ENST00000338791.11 linkuse as main transcript	c.147-35G>A		intron_variant		2	NM_000883.4		P20839-6

Frequencies

GnomAD3 genomes

AF:

0.0490

AC:

7461

AN:

152184

Hom.:

338

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0699

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0358

Gnomad ASJ

AF:

0.0637

Gnomad EAS

AF:

0.212

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.00762

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0270

Gnomad OTH

AF:

0.0517

GnomAD3 exomes

AF:

0.0569

AC:

14294

AN:

251382

Hom.:

878

AF XY:

0.0591

AC XY:

8038

AN XY:

135914

show subpopulations

Gnomad AFR exome

AF:

0.0714

Gnomad AMR exome

AF:

0.0293

Gnomad ASJ exome

AF:

0.0593

Gnomad EAS exome

AF:

0.218

Gnomad SAS exome

AF:

0.132

Gnomad FIN exome

AF:

0.00674

Gnomad NFE exome

AF:

0.0265

Gnomad OTH exome

AF:

0.0474

GnomAD4 exome

AF:

0.0385

AC:

56269

AN:

1459642

Hom.:

2140

Cov.:

AF XY:

0.0410

AC XY:

29750

AN XY:

726246

show subpopulations

Gnomad4 AFR exome

AF:

0.0714

Gnomad4 AMR exome

AF:

0.0306

Gnomad4 ASJ exome

AF:

0.0610

Gnomad4 EAS exome

AF:

0.180

Gnomad4 SAS exome

AF:

0.126

Gnomad4 FIN exome

AF:

0.00785

Gnomad4 NFE exome

AF:

0.0261

Gnomad4 OTH exome

AF:

0.0516

GnomAD4 genome

AF:

0.0490

AC:

7459

AN:

152302

Hom.:

338

Cov.:

AF XY:

0.0504

AC XY:

3755

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.0698

Gnomad4 AMR

AF:

0.0358

Gnomad4 ASJ

AF:

0.0637

Gnomad4 EAS

AF:

0.212

Gnomad4 SAS

AF:

0.133

Gnomad4 FIN

AF:

0.00762

Gnomad4 NFE

AF:

0.0270

Gnomad4 OTH

AF:

0.0516

Alfa

AF:

0.0389

Hom.:

Bravo

AF:

0.0516

Asia WGS

AF:

0.157

AC:

547

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.93

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over