2-200896214-T-G

Variant names:

• chr2-200896214-T-G
• rs13384245
• NM_001369441.2:c.726+824T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001369441.2. 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
	NIF3L1	NM_001369441.2	MANE Select	c.726+824T>G		intron	N/A	NP_001356370.1
	NIF3L1	NM_001136039.2		c.726+824T>G		intron	N/A	NP_001129511.1
	NIF3L1	NM_001369442.1		c.726+824T>G		intron	N/A	NP_001356371.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NIF3L1	ENST00000409020.6	TSL:5 MANE Select	c.726+824T>G		intron	N/A	ENSP00000386394.1
	NIF3L1	ENST00000359683.8	TSL:1	c.645+824T>G		intron	N/A	ENSP00000352711.4
	NIF3L1	ENST00000409588.1	TSL:1	c.726+824T>G		intron	N/A	ENSP00000387021.1

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

African (AFR) AF: 0.204 AC: 8442 AN: 41478

American (AMR) AF: 0.141 AC: 2154 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3472

East Asian (EAS) AF: 0.00830 AC: 43 AN: 5180

South Asian (SAS) AF: 0.0684 AC: 330 AN: 4822

European-Finnish (FIN) AF: 0.164 AC: 1736 AN: 10564

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11435 AN: 67980

Other (OTH) AF: 0.170 AC: 358 AN: 2106

Alfa AF: 0.165 Hom.: 5654

Bravo AF: 0.170

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.6
DANN	Benign	0.83
PhyloP100		-0.086
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: rs13384245; hg19: chr2-201760937;