3-16367271-C-T

Variant names:

• chr3-16367271-C-T
• rs689953
• NM_015150.2:c.1030+2805G>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.1030+2805G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 149,222 control chromosomes in the GnomAD database, including 20,684 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 0.53 (20684 hom., cov: 32)
• Consequence: RFTN1 NM_015150.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 9 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=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RFTN1	NM_015150.2	MANE Select	c.1030+2805G>A		intron	N/A	NP_055965.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RFTN1	ENST00000334133.9	TSL:1 MANE Select	c.1030+2805G>A		intron	N/A	ENSP00000334153.4
	RFTN1	ENST00000432519.5	TSL:1	c.922+2805G>A		intron	N/A	ENSP00000403926.1
	RFTN1	ENST00000483671.1	TSL:2	n.309+2805G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.526 AC: 78430 AN: 149112 Hom.: 20674 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.526 AC: 78477 AN: 149222 Hom.: 20684 Cov.: 32 AF XY: 0.517 AC XY: 37435 AN XY: 72458

African (AFR) AF: 0.536 AC: 22083 AN: 41194

American (AMR) AF: 0.459 AC: 6762 AN: 14734

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 1982 AN: 3416

East Asian (EAS) AF: 0.350 AC: 1763 AN: 5030

South Asian (SAS) AF: 0.311 AC: 1425 AN: 4578

European-Finnish (FIN) AF: 0.474 AC: 4724 AN: 9972

Middle Eastern (MID) AF: 0.569 AC: 165 AN: 290

European-Non Finnish (NFE) AF: 0.565 AC: 37845 AN: 67026

Other (OTH) AF: 0.556 AC: 1159 AN: 2084

Alfa AF: 0.546 Hom.: 44468

Bravo AF: 0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.84
PhyloP100		0.16
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: rs689953; hg19: chr3-16408778;