chr1-235981454-C-A

Position:

• chr1-235981454-C-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_002508.3(NID1):​c.3227+157G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,174 control chromosomes in the GnomAD database, including 4,031 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.21 (4031 hom., cov: 33)
• Consequence: NID1 NM_002508.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.265

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 1-235981454-C-A is Benign according to our data. Variant chr1-235981454-C-A is described in ClinVar as [Benign]. Clinvar id is 1237223.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NID1	NM_002508.3	c.3227+157G>T		intron_variant		ENST00000264187.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NID1	ENST00000264187.7	c.3227+157G>T		intron_variant		1	NM_002508.3	P1
NID1	ENST00000366595.7	c.2828+157G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32232 AN: 152056 Hom.: 4030 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0817

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.217

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.212 AC: 32245 AN: 152174 Hom.: 4031 Cov.: 33 AF XY: 0.213 AC XY: 15859 AN XY: 74394

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.219

Alfa AF: 0.183 Hom.: 4122

Bravo AF: 0.219

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.43

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

LitVar

Other links and lift over

dbSNP: rs3820558; hg19: chr1-236144754;