chr1-236016569-A-G

Position:

• chr1-236016569-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000264187.7(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 ENST00000264187.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NID1	NM_002508.3	c.2254+579T>C		intron_variant		ENST00000264187.7	NP_002499.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NID1	ENST00000264187.7	c.2254+579T>C		intron_variant		1	NM_002508.3	ENSP00000264187	P1
NID1	ENST00000366595.7	c.2128+7501T>C		intron_variant		1		ENSP00000355554

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

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.561

Alfa AF: 0.503 Hom.: 38041

Bravo AF: 0.603

Asia WGS AF: 0.735 AC: 2554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.51

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