rs1902249

Positions:

• chr2-197656632-T-C
• chr2-197656632-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144629.3(RFTN2):​c.140-9966A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,956 control chromosomes in the GnomAD database, including 35,574 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 0.68 (35574 hom., cov: 31)
• Consequence: RFTN2 NM_144629.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RFTN2	NM_144629.3	c.140-9966A>G		intron_variant		ENST00000295049.9	NP_653230.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RFTN2	ENST00000295049.9	c.140-9966A>G		intron_variant		1	NM_144629.3	ENSP00000295049.3
RFTN2	ENST00000429081.1	c.140-9966A>G		intron_variant		4		ENSP00000398128.1

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103397 AN: 151838 Hom.: 35550 Cov.: 31

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.681 AC: 103472 AN: 151956 Hom.: 35574 Cov.: 31 AF XY: 0.677 AC XY: 50306 AN XY: 74278

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.714

Alfa AF: 0.683 Hom.: 16853

Bravo AF: 0.686

Asia WGS AF: 0.587 AC: 2042 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.51

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

Publications

LitVar

Other links and lift over

dbSNP: rs1902249; hg19: chr2-198521356;