chr1-235979265-T-C

Position:

• chr1-235979265-T-C

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.3510-158A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 151,942 control chromosomes in the GnomAD database, including 50,517 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.81 (50517 hom., cov: 30)
• Consequence: NID1 NM_002508.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.41

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=-0.9).
• BP6: Variant 1-235979265-T-C is Benign according to our data. Variant chr1-235979265-T-C is described in ClinVar as [Benign]. Clinvar id is 1282027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NID1	NM_002508.3	c.3510-158A>G		intron_variant		ENST00000264187.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NID1	ENST00000264187.7	c.3510-158A>G		intron_variant		1	NM_002508.3	P1
NID1	ENST00000366595.7	c.3111-158A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123453 AN: 151824 Hom.: 50477 Cov.: 30

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.813 AC: 123550 AN: 151942 Hom.: 50517 Cov.: 30 AF XY: 0.811 AC XY: 60222 AN XY: 74258

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.734

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.802

Alfa AF: 0.799 Hom.: 9543

Bravo AF: 0.822

Asia WGS AF: 0.656 AC: 2284 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	-0.90
CADD	Benign	0.034
DANN	Benign	0.63

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: rs1536132; hg19: chr1-236142565;