2-197649153-C-T

Variant names:

• chr2-197649153-C-T
• rs7564924
• NM_144629.3:c.140-2487G>A

Variant summary

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

The NM_144629.3(RFTN2):​c.140-2487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,108 control chromosomes in the GnomAD database, including 37,680 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 (37680 hom., cov: 32)
• Consequence: RFTN2 NM_144629.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 9 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144629.3. 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
	RFTN2	NM_144629.3	MANE Select	c.140-2487G>A		intron	N/A	NP_653230.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RFTN2	ENST00000295049.9	TSL:1 MANE Select	c.140-2487G>A		intron	N/A	ENSP00000295049.3
	RFTN2	ENST00000429081.1	TSL:4	c.140-2487G>A		intron	N/A	ENSP00000398128.1
	ENSG00000222017	ENST00000721462.1		n.213+8652C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106223 AN: 151990 Hom.: 37646 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.682

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: 106309 AN: 152108 Hom.: 37680 Cov.: 32 AF XY: 0.695 AC XY: 51643 AN XY: 74330

African (AFR) AF: 0.800 AC: 33197 AN: 41520

American (AMR) AF: 0.648 AC: 9906 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2615 AN: 3472

East Asian (EAS) AF: 0.475 AC: 2458 AN: 5174

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

European-Finnish (FIN) AF: 0.588 AC: 6194 AN: 10538

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

European-Non Finnish (NFE) AF: 0.682 AC: 46335 AN: 67980

Other (OTH) AF: 0.725 AC: 1533 AN: 2114

Alfa AF: 0.685 Hom.: 20472

Bravo AF: 0.706

Asia WGS AF: 0.591 AC: 2057 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.31
PhyloP100		0.23
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: rs7564924; hg19: chr2-198513877;