Genetic Variant NID1:c.3510-4G>A (chr1-235979111-C-T) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_002508.3(NID1):c.3510-4G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 1,586,162 control chromosomes in the GnomAD database, including 158 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0090 ( 12 hom., cov: 32)

Exomes 𝑓: 0.012 ( 146 hom. )

Consequence

NID1
NM_002508.3 splice_region, intron

Scores

Splicing: ADA: 0.00002990

Clinical Significance

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

Conservation

PhyloP100: -0.116

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 made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 1-235979111-C-T is Benign according to our data. Variant chr1-235979111-C-T is described in ClinVar as [Benign]. Clinvar id is 780005.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NID1	NM_002508.3 link	c.3510-4G>A		splice_region_variant, intron_variant	Intron 18 of 19	ENST00000264187.7	NP_002499.2	P14543-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NID1	ENST00000264187.7 link	c.3510-4G>A		splice_region_variant, intron_variant	Intron 18 of 19	1	NM_002508.3	ENSP00000264187.6		P14543-1
NID1	ENST00000366595.7 link	c.3111-4G>A		splice_region_variant, intron_variant	Intron 15 of 16	1		ENSP00000355554.3		P14543-2

Frequencies

GnomAD3 genomes

AF:

0.00897

AC:

1365

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00203

Gnomad AMI

AF:

0.0407

Gnomad AMR

AF:

0.00635

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.0261

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0124

Gnomad OTH

AF:

0.00907

GnomAD3 exomes

AF:

0.00926

AC:

2323

AN:

250866

Hom.:

AF XY:

0.00904

AC XY:

1226

AN XY:

135560

show subpopulations

Gnomad AFR exome

AF:

0.00179

Gnomad AMR exome

AF:

0.00463

Gnomad ASJ exome

AF:

0.00149

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000621

Gnomad FIN exome

AF:

0.0275

Gnomad NFE exome

AF:

0.0127

Gnomad OTH exome

AF:

0.0101

GnomAD4 exome

AF:

0.0116

AC:

16680

AN:

1433912

Hom.:

146

Cov.:

AF XY:

0.0112

AC XY:

7991

AN XY:

715272

show subpopulations

Gnomad4 AFR exome

AF:

0.00146

Gnomad4 AMR exome

AF:

0.00439

Gnomad4 ASJ exome

AF:

0.00154

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.000805

Gnomad4 FIN exome

AF:

0.0262

Gnomad4 NFE exome

AF:

0.0132

Gnomad4 OTH exome

AF:

0.0101

GnomAD4 genome

AF:

0.00897

AC:

1365

AN:

152250

Hom.:

Cov.:

AF XY:

0.00884

AC XY:

658

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.00202

Gnomad4 AMR

AF:

0.00634

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.0261

Gnomad4 NFE

AF:

0.0124

Gnomad4 OTH

AF:

0.00898

Alfa

AF:

0.0102

Hom.:

Bravo

AF:

0.00811

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.0119

EpiControl

AF:

0.0115

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jan 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

NID1: BP4, BS1, BS2 -

Jun 15, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.8

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000030

dbscSNV1_RF

Benign

0.0

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

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