Genetic Variant DYNC1I2:c.512-6_512-4dupTTT (chr2-171725598-G-GTTT) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001378.3(DYNC1I2):c.512-6_512-4dupTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 894,474 control chromosomes in the GnomAD database, including 16 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000057 ( 0 hom., cov: 22)

Exomes 𝑓: 0.0016 ( 16 hom. )

Consequence

DYNC1I2
NM_001378.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.112

Publications

0 publications found

Variant links:

Genes affected

DYNC1I2 (HGNC:2964): (dynein cytoplasmic 1 intermediate chain 2) This gene encodes a member of the dynein intermediate chain family. The encoded protein is a non-catalytic component of the cytoplasmic dynein 1 complex, which acts as a retrograde microtubule motor to transport organelles and vesicles. A pseudogene of this gene is located on chromosome 10. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

DYNC1I2 Gene-Disease associations (from GenCC):

neurodevelopmental disorder with microcephaly and structural brain anomalies
Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P

DYNC1I2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 16 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNC1I2	NM_001378.3 link	c.512-6_512-4dupTTT		splice_region_variant, intron_variant	Intron 7 of 17	ENST00000397119.8	NP_001369.1	Q13409-1A0A140VKE9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNC1I2	ENST00000397119.8 link	c.512-20_512-19insTTT		intron_variant	Intron 7 of 17	1	NM_001378.3	ENSP00000380308.3		Q13409-1

Frequencies

GnomAD3 genomes

AF:

0.0000566

AC:

AN:

106072

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000925

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000992

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00398

AC:

162

AN:

40656

AF XY:

0.00457

show subpopulations

Gnomad AFR exome

AF:

0.00298

Gnomad AMR exome

AF:

0.00511

Gnomad ASJ exome

AF:

0.00594

Gnomad EAS exome

AF:

0.00467

Gnomad FIN exome

AF:

0.00307

Gnomad NFE exome

AF:

0.00345

Gnomad OTH exome

AF:

0.00660

GnomAD4 exome

AF:

0.00159

AC:

1254

AN:

788402

Hom.:

Cov.:

AF XY:

0.00174

AC XY:

693

AN XY:

398426

show subpopulations

African (AFR)

AF:

0.000702

AC:

AN:

15666

American (AMR)

AF:

0.00177

AC:

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.00226

AC:

AN:

15020

East Asian (EAS)

AF:

0.000590

AC:

AN:

25430

South Asian (SAS)

AF:

0.00666

AC:

263

AN:

39478

European-Finnish (FIN)

AF:

0.00221

AC:

AN:

36186

Middle Eastern (MID)

AF:

0.00260

AC:

AN:

2306

European-Non Finnish (NFE)

AF:

0.00125

AC:

759

AN:

604952

Other (OTH)

AF:

0.00173

AC:

AN:

34092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.414

Heterozygous variant carriers

108

162

216

270

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000566

AC:

AN:

106072

Hom.:

Cov.:

AF XY:

0.0000984

AC XY:

AN XY:

50832

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

27672

American (AMR)

AF:

0.0000925

AC:

AN:

10806

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2660

East Asian (EAS)

AF:

0.00

AC:

AN:

3646

South Asian (SAS)

AF:

0.00

AC:

AN:

3466

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5108

Middle Eastern (MID)

AF:

0.00

AC:

AN:

202

European-Non Finnish (NFE)

AF:

0.0000992

AC:

AN:

50380

Other (OTH)

AF:

0.00

AC:

AN:

1454

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.317

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.11

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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2-171725598-GTTTTTT-GTTTTTTTTT

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