rs1598469

Variant names:

• chr2-197650934-T-C
• rs1598469
• NM_144629.3:c.140-4268A>G

Variant summary

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

The NM_144629.3(RFTN2):​c.140-4268A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,116 control chromosomes in the GnomAD database, including 37,637 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 0.70 (37637 hom., cov: 32)
• Consequence: RFTN2 NM_144629.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 6 publications found

Genes affected

RFTN2 (HGNC:26402): (raftlin family member 2) Predicted to act upstream of or within dsRNA transport and response to exogenous dsRNA. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000222017 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RFTN2	NM_144629.3	c.140-4268A>G		intron_variant	Intron 1 of 8	ENST00000295049.9	NP_653230.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RFTN2	ENST00000295049.9	c.140-4268A>G		intron_variant	Intron 1 of 8	1	NM_144629.3	ENSP00000295049.3
RFTN2	ENST00000429081.1	c.140-4268A>G		intron_variant	Intron 2 of 3	4		ENSP00000398128.1
ENSG00000222017	ENST00000721462.1	n.213+10433T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106167 AN: 151998 Hom.: 37603 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.699 AC: 106253 AN: 152116 Hom.: 37637 Cov.: 32 AF XY: 0.694 AC XY: 51627 AN XY: 74362

African (AFR) AF: 0.799 AC: 33164 AN: 41500

American (AMR) AF: 0.648 AC: 9908 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2611 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2449 AN: 5166

South Asian (SAS) AF: 0.657 AC: 3169 AN: 4826

European-Finnish (FIN) AF: 0.586 AC: 6198 AN: 10570

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46317 AN: 67972

Other (OTH) AF: 0.725 AC: 1535 AN: 2116

Alfa AF: 0.689 Hom.: 19034

Bravo AF: 0.706

Asia WGS AF: 0.591 AC: 2056 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-0.70
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: rs1598469; hg19: chr2-198515658;