3-16354161-C-T

Variant names:

• chr3-16354161-C-T
• rs690037
• NM_015150.2:c.1146+3771G>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.1146+3771G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,928 control chromosomes in the GnomAD database, including 18,267 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 0.49 (18267 hom., cov: 31)
• Consequence: RFTN1 NM_015150.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 21 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015150.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RFTN1	NM_015150.2	MANE Select	c.1146+3771G>A		intron	N/A	NP_055965.1	Q14699

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RFTN1	ENST00000334133.9	TSL:1 MANE Select	c.1146+3771G>A		intron	N/A	ENSP00000334153.4	Q14699
	RFTN1	ENST00000432519.5	TSL:1	c.1038+3771G>A		intron	N/A	ENSP00000403926.1	G3XAJ6
	RFTN1	ENST00000856941.1		c.1146+3771G>A		intron	N/A	ENSP00000527000.1

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74166 AN: 151810 Hom.: 18247 Cov.: 31

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.489 AC: 74229 AN: 151928 Hom.: 18267 Cov.: 31 AF XY: 0.491 AC XY: 36478 AN XY: 74256

African (AFR) AF: 0.533 AC: 22092 AN: 41418

American (AMR) AF: 0.432 AC: 6604 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1652 AN: 3470

East Asian (EAS) AF: 0.516 AC: 2662 AN: 5156

South Asian (SAS) AF: 0.447 AC: 2152 AN: 4812

European-Finnish (FIN) AF: 0.523 AC: 5519 AN: 10562

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32148 AN: 67922

Other (OTH) AF: 0.438 AC: 924 AN: 2108

Alfa AF: 0.474 Hom.: 37709

Bravo AF: 0.482

Asia WGS AF: 0.474 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.35
PhyloP100		-1.0
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: rs690037; hg19: chr3-16395668;