Genetic Variant NID1:c.3386-58dupT (chr1-235980002-C-CA) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002508.3(NID1):c.3386-58dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,570,962 control chromosomes in the GnomAD database, including 36,285 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 5271 hom., cov: 26)

Exomes 𝑓: 0.20 ( 31014 hom. )

Consequence

NID1
NM_002508.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.334

Publications

3 publications found

Variant links:

Genes affected

NID1 (HGNC:7821): (nidogen 1) This gene encodes a member of the nidogen family of basement membrane glycoproteins. The protein interacts with several other components of basement membranes, and may play a role in cell interactions with the extracellular matrix. [provided by RefSeq, Jul 2008]

NID1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 1-235980002-C-CA is Benign according to our data. Variant chr1-235980002-C-CA is described in ClinVar as Benign. ClinVar VariationId is 1245717.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002508.3. 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
	NID1	NM_002508.3	MANE Select	c.3386-58dupT		intron	N/A	NP_002499.2	P14543-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NID1	ENST00000264187.7	TSL:1 MANE Select	c.3386-58_3386-57insT	intron	N/A	ENSP00000264187.6	P14543-1
NID1	ENST00000366595.7	TSL:1	c.2987-58_2987-57insT	intron	N/A	ENSP00000355554.3	P14543-2
NID1	ENST00000856588.1		c.3383-58_3383-57insT	intron	N/A	ENSP00000526647.1

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36646

AN:

151268

Hom.:

5265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.340

Gnomad AMI

AF:

0.0802

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.623

Gnomad SAS

AF:

0.276

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.177

Gnomad OTH

AF:

0.246

GnomAD4 exome

AF:

0.200

AC:

283250

AN:

1419578

Hom.:

31014

AF XY:

0.200

AC XY:

141348

AN XY:

705660

show subpopulations

African (AFR)

AF:

0.335

AC:

10694

AN:

31928

American (AMR)

AF:

0.246

AC:

10444

AN:

42390

Ashkenazi Jewish (ASJ)

AF:

0.150

AC:

3800

AN:

25380

East Asian (EAS)

AF:

0.615

AC:

23106

AN:

37564

South Asian (SAS)

AF:

0.251

AC:

20971

AN:

83574

European-Finnish (FIN)

AF:

0.142

AC:

7478

AN:

52608

Middle Eastern (MID)

AF:

0.208

AC:

1168

AN:

5614

European-Non Finnish (NFE)

AF:

0.178

AC:

192431

AN:

1082170

Other (OTH)

AF:

0.226

AC:

13158

AN:

58350

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

9945

19889

29834

39778

49723

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7176

14352

21528

28704

35880

<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:

0.242

AC:

36674

AN:

151384

Hom.:

5271

Cov.:

AF XY:

0.243

AC XY:

17945

AN XY:

73908

show subpopulations

African (AFR)

AF:

0.340

AC:

14016

AN:

41246

American (AMR)

AF:

0.226

AC:

3428

AN:

15198

Ashkenazi Jewish (ASJ)

AF:

0.153

AC:

530

AN:

3456

East Asian (EAS)

AF:

0.622

AC:

3184

AN:

5120

South Asian (SAS)

AF:

0.275

AC:

1320

AN:

4806

European-Finnish (FIN)

AF:

0.150

AC:

1565

AN:

10438

Middle Eastern (MID)

AF:

0.201

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.177

AC:

11977

AN:

67806

Other (OTH)

AF:

0.247

AC:

522

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1291

2582

3874

5165

6456

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<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:

0.0595

Hom.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.33

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over