3-16366982-T-C

Variant names:

• chr3-16366982-T-C
• rs12635698
• NM_015150.2:c.1030+3094A>G

Variant summary

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

The NM_015150.2(RFTN1):​c.1030+3094A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,486 control chromosomes in the GnomAD database, including 4,643 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 0.22 (4643 hom., cov: 33)
• Consequence: RFTN1 NM_015150.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 14 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]

ENSG00000287377 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RFTN1	NM_015150.2	c.1030+3094A>G		intron_variant	Intron 6 of 9	ENST00000334133.9	NP_055965.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RFTN1	ENST00000334133.9	c.1030+3094A>G		intron_variant	Intron 6 of 9	1	NM_015150.2	ENSP00000334153.4
RFTN1	ENST00000432519.5	c.922+3094A>G		intron_variant	Intron 5 of 8	1		ENSP00000403926.1
RFTN1	ENST00000483671.1	n.309+3094A>G		intron_variant	Intron 2 of 5	2
ENSG00000287377	ENST00000653928.1	n.348-2697T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32846 AN: 151366 Hom.: 4632 Cov.: 33

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0593

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.217 AC: 32901 AN: 151486 Hom.: 4643 Cov.: 33 AF XY: 0.197 AC XY: 14515 AN XY: 73762

African (AFR) AF: 0.466 AC: 19034 AN: 40882

American (AMR) AF: 0.160 AC: 2452 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 903 AN: 3460

East Asian (EAS) AF: 0.0307 AC: 159 AN: 5186

South Asian (SAS) AF: 0.127 AC: 609 AN: 4804

European-Finnish (FIN) AF: 0.0593 AC: 629 AN: 10606

Middle Eastern (MID) AF: 0.262 AC: 76 AN: 290

European-Non Finnish (NFE) AF: 0.125 AC: 8473 AN: 67962

Other (OTH) AF: 0.222 AC: 468 AN: 2108

Alfa AF: 0.153 Hom.: 6807

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
DANN	Benign	0.66
PhyloP100		0.33
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: rs12635698; hg19: chr3-16408489;