Genetic Variant IQCN:c.3178-1874T>G (chr19-18259980-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001145304.2(IQCN):c.3178-1874T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 152,500 control chromosomes in the GnomAD database, including 846 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 0.091 ( 841 hom., cov: 34)

Exomes 𝑓: 0.17 ( 5 hom. )

Consequence

IQCN
NM_001145304.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0340

Publications

3 publications found

Variant links:

Genes affected

IQCN (HGNC:29350): (IQ motif containing N) Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

IQCN links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
IQCN	NM_001145304.2 link	c.3178-1874T>G	intron_variant	Intron 3 of 3	ENST00000392413.5	NP_001138776.1	Q9H0B3-4
IQCN	NM_025249.4 link	c.2617-1874T>G	intron_variant	Intron 3 of 3		NP_079525.1	Q9H0B3-1
IQCN	NM_001145305.2 link	c.2479-1874T>G	intron_variant	Intron 3 of 3		NP_001138777.1	Q9H0B3-5A0JP07
IQCN	XM_005260084.2 link	c.3178-1874T>G	intron_variant	Intron 3 of 3		XP_005260141.1	Q9H0B3-4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
IQCN	ENST00000392413.5 link	c.3178-1874T>G	intron_variant	Intron 3 of 3	1	NM_001145304.2	ENSP00000376213.2	Q9H0B3-4
IQCN	ENST00000600328.7 link	c.2617-1874T>G	intron_variant	Intron 3 of 3	1		ENSP00000470780.1	Q9H0B3-1
IQCN	ENST00000599638.2 link	n.2639T>G	non_coding_transcript_exon_variant	Exon 1 of 1	6
IQCN	ENST00000600359.7 link	c.2479-1874T>G	intron_variant	Intron 3 of 3	2		ENSP00000472912.1	Q9H0B3-5

Frequencies

GnomAD3 genomes

AF:

0.0914

AC:

13921

AN:

152232

Hom.:

842

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0205

Gnomad AMI

AF:

0.0680

Gnomad AMR

AF:

0.0612

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.0775

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.0872

GnomAD4 exome

AF:

0.167

AC:

AN:

150

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.185

AC:

AN:

130

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0914

AC:

13918

AN:

152350

Hom.:

841

Cov.:

AF XY:

0.0925

AC XY:

6894

AN XY:

74502

show subpopulations

African (AFR)

AF:

0.0205

AC:

851

AN:

41594

American (AMR)

AF:

0.0611

AC:

935

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

451

AN:

3472

East Asian (EAS)

AF:

0.00116

AC:

AN:

5190

South Asian (SAS)

AF:

0.0778

AC:

376

AN:

4834

European-Finnish (FIN)

AF:

0.188

AC:

1995

AN:

10616

Middle Eastern (MID)

AF:

0.0612

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.133

AC:

9043

AN:

68024

Other (OTH)

AF:

0.0858

AC:

181

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

662

1324

1985

2647

3309

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.112

Hom.:

781

Bravo

AF:

0.0784

Asia WGS

AF:

0.0300

AC:

108

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.6

(source)

DANN

Benign

0.72

PhyloP100

-0.034

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over