chr1-235980002-C-CA

Position:

• chr1-235980002-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_002508.3(NID1):​c.3386-58_3386-57insT 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.334

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]

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NID1	NM_002508.3	c.3386-58_3386-57insT		intron_variant		ENST00000264187.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NID1	ENST00000264187.7	c.3386-58_3386-57insT		intron_variant		1	NM_002508.3	P1
NID1	ENST00000366595.7	c.2987-58_2987-57insT		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36646 AN: 151268 Hom.: 5265 Cov.: 26

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

Gnomad4 AFR exome AF: 0.335

Gnomad4 AMR exome AF: 0.246

Gnomad4 ASJ exome AF: 0.150

Gnomad4 EAS exome AF: 0.615

Gnomad4 SAS exome AF: 0.251

Gnomad4 FIN exome AF: 0.142

Gnomad4 NFE exome AF: 0.178

Gnomad4 OTH exome AF: 0.226

GnomAD4 genome AF: 0.242 AC: 36674 AN: 151384 Hom.: 5271 Cov.: 26 AF XY: 0.243 AC XY: 17945 AN XY: 73908

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.247

Alfa AF: 0.0595 Hom.: 59

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

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

LitVar

Other links and lift over

dbSNP: rs3831989; hg19: chr1-236143302;