NM_015150.2:c.146-4014G>A

Variant names:

• chr3-16438051-C-T
• rs9839841
• NM_015150.2:c.146-4014G>A

Variant summary

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

The NM_015150.2(RFTN1):​c.146-4014G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,110 control chromosomes in the GnomAD database, including 3,001 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 0.19 (3001 hom., cov: 31)
• Consequence: RFTN1 NM_015150.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 5 publications found

Genes affected

RFTN1 (HGNC:30278): (raftlin, lipid raft linker 1) Enables double-stranded RNA binding activity. Involved in B cell receptor signaling pathway; membrane raft assembly; and positive regulation of growth rate. Acts upstream of or within dsRNA transport; response to exogenous dsRNA; and toll-like receptor 3 signaling pathway. Located in endosome; membrane raft; and plasma membrane. Part of protein-containing complex. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RFTN1	NM_015150.2	c.146-4014G>A		intron_variant	Intron 2 of 9	ENST00000334133.9	NP_055965.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RFTN1	ENST00000334133.9	c.146-4014G>A		intron_variant	Intron 2 of 9	1	NM_015150.2	ENSP00000334153.4

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28543 AN: 151992 Hom.: 2992 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.188 AC: 28587 AN: 152110 Hom.: 3001 Cov.: 31 AF XY: 0.187 AC XY: 13945 AN XY: 74376

African (AFR) AF: 0.256 AC: 10635 AN: 41464

American (AMR) AF: 0.216 AC: 3296 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3462

East Asian (EAS) AF: 0.224 AC: 1160 AN: 5176

South Asian (SAS) AF: 0.0870 AC: 420 AN: 4828

European-Finnish (FIN) AF: 0.131 AC: 1390 AN: 10596

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10741 AN: 67986

Other (OTH) AF: 0.186 AC: 392 AN: 2112

Alfa AF: 0.240 Hom.: 847

Bravo AF: 0.203

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.83
PhyloP100		-0.39
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: rs9839841; hg19: chr3-16479558;