rs13421776

Positions:

• chr2-200896179-G-C

Variant summary

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

The NM_001369441.2(NIF3L1):​c.726+789G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,946 control chromosomes in the GnomAD database, including 4,705 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 0.23 (4705 hom., cov: 31)
• Consequence: NIF3L1 NM_001369441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIF3L1	NM_001369441.2	c.726+789G>C		intron_variant		ENST00000409020.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIF3L1	ENST00000409020.6	c.726+789G>C		intron_variant		5	NM_001369441.2	P1

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34526 AN: 151828 Hom.: 4697 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.00868

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.228 AC: 34576 AN: 151946 Hom.: 4705 Cov.: 31 AF XY: 0.223 AC XY: 16561 AN XY: 74286

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.00870

Gnomad4 SAS AF: 0.0809

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.219

Alfa AF: 0.217 Hom.: 525

Bravo AF: 0.236

Asia WGS AF: 0.0730 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.66

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: rs13421776; hg19: chr2-201760902;