2-200896214-T-G

Position:

• chr2-200896214-T-G

Variant summary

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

The NM_001369441.2(NIF3L1):​c.726+824T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,078 control chromosomes in the GnomAD database, including 2,321 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 0.17 (2321 hom., cov: 31)
• Consequence: NIF3L1 NM_001369441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

Genes affected

NIF3L1 (HGNC:13390): (NGG1 interacting factor 3 like 1) Enables identical protein binding activity. Involved in positive regulation of transcription, DNA-templated. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NIF3L1	NM_001369441.2	c.726+824T>G		intron_variant		ENST00000409020.6	NP_001356370.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NIF3L1	ENST00000409020.6	c.726+824T>G		intron_variant		5	NM_001369441.2	ENSP00000386394.1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25403 AN: 151960 Hom.: 2319 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00828

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.167 AC: 25417 AN: 152078 Hom.: 2321 Cov.: 31 AF XY: 0.164 AC XY: 12173 AN XY: 74366

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.00830

Gnomad4 SAS AF: 0.0684

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.170

Alfa AF: 0.163 Hom.: 2134

Bravo AF: 0.170

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.6
DANN	Benign	0.83

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: rs13384245; hg19: chr2-201760937;