rs689662

Variant names:

• chr3-16372691-G-A
• rs689662
• NM_015150.2:c.827-2412C>T

Variant summary

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

The NM_015150.2(RFTN1):​c.827-2412C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,106 control chromosomes in the GnomAD database, including 30,805 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 0.62 (30805 hom., cov: 32)
• Consequence: RFTN1 NM_015150.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359
• Publications: 17 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RFTN1	NM_015150.2	c.827-2412C>T		intron_variant	Intron 5 of 9	ENST00000334133.9	NP_055965.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RFTN1	ENST00000334133.9	c.827-2412C>T		intron_variant	Intron 5 of 9	1	NM_015150.2	ENSP00000334153.4
RFTN1	ENST00000432519.5	c.719-2412C>T		intron_variant	Intron 4 of 8	1		ENSP00000403926.1

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94263 AN: 151988 Hom.: 30782 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.620 AC: 94335 AN: 152106 Hom.: 30805 Cov.: 32 AF XY: 0.606 AC XY: 45046 AN XY: 74368

African (AFR) AF: 0.811 AC: 33664 AN: 41494

American (AMR) AF: 0.500 AC: 7644 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1910 AN: 3470

East Asian (EAS) AF: 0.363 AC: 1878 AN: 5176

South Asian (SAS) AF: 0.304 AC: 1462 AN: 4816

European-Finnish (FIN) AF: 0.454 AC: 4804 AN: 10590

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40799 AN: 67974

Other (OTH) AF: 0.626 AC: 1319 AN: 2106

Alfa AF: 0.628 Hom.: 25400

Bravo AF: 0.638

Asia WGS AF: 0.379 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.8
DANN	Benign	0.68
PhyloP100		0.36
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: rs689662; hg19: chr3-16414198;