chr1-235980961-T-C

Position:

• chr1-235980961-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_002508.3(NID1):​c.3228-308A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,056 control chromosomes in the GnomAD database, including 5,242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (5242 hom., cov: 32)
• Consequence: NID1 NM_002508.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.31

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 1-235980961-T-C is Benign according to our data. Variant chr1-235980961-T-C is described in ClinVar as [Benign]. Clinvar id is 1241800.Status of the report is criteria_provided_single_submitter, 1 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.3228-308A>G		intron_variant		ENST00000264187.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NID1	ENST00000264187.7	c.3228-308A>G		intron_variant		1	NM_002508.3	P1
NID1	ENST00000366595.7	c.2829-308A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36469 AN: 151938 Hom.: 5234 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.240 AC: 36498 AN: 152056 Hom.: 5242 Cov.: 32 AF XY: 0.240 AC XY: 17874 AN XY: 74362

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.245

Alfa AF: 0.201 Hom.: 432

Bravo AF: 0.252

Asia WGS AF: 0.396 AC: 1376 AN: 3478

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

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.39

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: rs3820557; hg19: chr1-236144261;