dbSNP rs16833075: NID1:c.2528-105A>C (chr1-235993977-T-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002508.3(NID1):c.2528-105A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 923,086 control chromosomes in the GnomAD database, including 23,471 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3453 hom., cov: 33)

Exomes 𝑓: 0.20 ( 20018 hom. )

Consequence

NID1
NM_002508.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0900

Publications

7 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

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

BP6

Variant 1-235993977-T-G is Benign according to our data. Variant chr1-235993977-T-G is described in ClinVar as Benign. ClinVar VariationId is 1282638.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.546 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.2528-105A>C		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.2528-105A>C	intron	N/A	ENSP00000264187.6	P14543-1
NID1	ENST00000366595.7	TSL:1	c.2129-105A>C	intron	N/A	ENSP00000355554.3	P14543-2
NID1	ENST00000856588.1		c.2525-105A>C	intron	N/A	ENSP00000526647.1

Frequencies

GnomAD3 genomes

AF:

0.197

AC:

29970

AN:

152108

Hom.:

3452

Cov.:

show subpopulations

Gnomad AFR

AF:

0.196

Gnomad AMI

AF:

0.0921

Gnomad AMR

AF:

0.200

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.562

Gnomad SAS

AF:

0.360

Gnomad FIN

AF:

0.141

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.207

GnomAD4 exome

AF:

0.203

AC:

156269

AN:

770860

Hom.:

20018

AF XY:

0.207

AC XY:

80529

AN XY:

388758

show subpopulations

African (AFR)

AF:

0.189

AC:

3513

AN:

18552

American (AMR)

AF:

0.217

AC:

4686

AN:

21554

Ashkenazi Jewish (ASJ)

AF:

0.132

AC:

2139

AN:

16180

East Asian (EAS)

AF:

0.584

AC:

18825

AN:

32236

South Asian (SAS)

AF:

0.327

AC:

17882

AN:

54690

European-Finnish (FIN)

AF:

0.137

AC:

5085

AN:

37182

Middle Eastern (MID)

AF:

0.178

AC:

752

AN:

4236

European-Non Finnish (NFE)

AF:

0.174

AC:

95490

AN:

549560

Other (OTH)

AF:

0.215

AC:

7897

AN:

36670

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

6381

12762

19144

25525

31906

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2714

5428

8142

10856

13570

<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:

0.197

AC:

29981

AN:

152226

Hom.:

3453

Cov.:

AF XY:

0.198

AC XY:

14773

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.196

AC:

8129

AN:

41532

American (AMR)

AF:

0.200

AC:

3053

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

452

AN:

3470

East Asian (EAS)

AF:

0.563

AC:

2905

AN:

5162

South Asian (SAS)

AF:

0.359

AC:

1732

AN:

4826

European-Finnish (FIN)

AF:

0.141

AC:

1498

AN:

10610

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11633

AN:

68010

Other (OTH)

AF:

0.208

AC:

439

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1202

2403

3605

4806

6008

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

332

664

996

1328

1660

<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:

0.184

Hom.:

8744

Bravo

AF:

0.201

Asia WGS

AF:

0.413

AC:

1435

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.6

(source)

DANN

Benign

0.62

PhyloP100

0.090

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over