NM_002508.3:c.2254+579T>C

Variant names:

• chr1-236016569-A-G
• rs3768080
• NM_002508.3:c.2254+579T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002508.3(NID1):​c.2254+579T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 152,000 control chromosomes in the GnomAD database, including 28,193 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.60 (28193 hom., cov: 31)
• Consequence: NID1 NM_002508.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253
• Publications: 23 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.744 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NID1	NM_002508.3	MANE Select	c.2254+579T>C		intron	N/A	NP_002499.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NID1	ENST00000264187.7	TSL:1 MANE Select	c.2254+579T>C		intron	N/A	ENSP00000264187.6
	NID1	ENST00000366595.7	TSL:1	c.2128+7501T>C		intron	N/A	ENSP00000355554.3

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90622 AN: 151882 Hom.: 28152 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.597 AC: 90722 AN: 152000 Hom.: 28193 Cov.: 31 AF XY: 0.601 AC XY: 44660 AN XY: 74276

African (AFR) AF: 0.746 AC: 30941 AN: 41450

American (AMR) AF: 0.617 AC: 9419 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1423 AN: 3466

East Asian (EAS) AF: 0.764 AC: 3948 AN: 5168

South Asian (SAS) AF: 0.665 AC: 3206 AN: 4818

European-Finnish (FIN) AF: 0.601 AC: 6341 AN: 10550

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33614 AN: 67966

Other (OTH) AF: 0.561 AC: 1185 AN: 2112

Alfa AF: 0.523 Hom.: 65194

Bravo AF: 0.603

Asia WGS AF: 0.735 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.51
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3768080; hg19: chr1-236179869; COSMIC: COSV51617248;