NM_001369441.2:c.865+210G>A

Variant names:

• chr2-200897424-G-A
• rs10204787
• NM_001369441.2:c.865+210G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001369441.2(NIF3L1):​c.865+210G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,048 control chromosomes in the GnomAD database, including 2,354 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 (2354 hom., cov: 32)
• Consequence: NIF3L1 NM_001369441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NIF3L1	NM_001369441.2	c.865+210G>A		intron_variant	Intron 5 of 6	ENST00000409020.6	NP_001356370.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NIF3L1	ENST00000409020.6	c.865+210G>A		intron_variant	Intron 5 of 6	5	NM_001369441.2	ENSP00000386394.1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25525 AN: 151930 Hom.: 2351 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.00829

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.168 AC: 25542 AN: 152048 Hom.: 2354 Cov.: 32 AF XY: 0.165 AC XY: 12249 AN XY: 74324

African (AFR) AF: 0.206 AC: 8554 AN: 41456

American (AMR) AF: 0.141 AC: 2159 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3470

East Asian (EAS) AF: 0.00831 AC: 43 AN: 5176

South Asian (SAS) AF: 0.0686 AC: 331 AN: 4826

European-Finnish (FIN) AF: 0.165 AC: 1744 AN: 10570

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

European-Non Finnish (NFE) AF: 0.168 AC: 11437 AN: 67978

Other (OTH) AF: 0.170 AC: 357 AN: 2104

Alfa AF: 0.170 Hom.: 3793

Bravo AF: 0.171

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	-0.95
CADD	Benign	0.028
DANN	Benign	0.21
PhyloP100		-0.94
PromoterAI		-0.016	Neutral
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: rs10204787; hg19: chr2-201762147;