dbSNP rs796203024: RTF1:p.Ala10Gly (chr15-41417144-C-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_015138.5(RTF1):c.29C>G(p.Ala10Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A10V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RTF1
NM_015138.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.36

Publications

0 publications found

Variant links:

Genes affected

RTF1 (HGNC:28996): (RTF1 homolog, Paf1/RNA polymerase II complex component) This locus may represent a gene involved in regulation of transcription elongation and chromatin remodeling, based on studies of similar proteins in other organisms. The encoded protein may bind single-stranded DNA. [provided by RefSeq, Sep 2010]

RTF1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.16095889).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015138.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RTF1	NM_015138.5	MANE Select	c.29C>G	p.Ala10Gly	missense	Exon 1 of 18	NP_055953.3	Q92541

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
RTF1	ENST00000389629.9	TSL:1 MANE Select	c.29C>G	p.Ala10Gly	missense	Exon 1 of 18	ENSP00000374280.4	Q92541
RTF1	ENST00000925186.1		c.29C>G	p.Ala10Gly	missense	Exon 1 of 17	ENSP00000595245.1
RTF1	ENST00000925187.1		c.29C>G	p.Ala10Gly	missense	Exon 1 of 17	ENSP00000595246.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1105580

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

525618

African (AFR)

AF:

0.00

AC:

AN:

23038

American (AMR)

AF:

0.00

AC:

AN:

8498

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14456

East Asian (EAS)

AF:

0.00

AC:

AN:

26830

South Asian (SAS)

AF:

0.00

AC:

AN:

22192

European-Finnish (FIN)

AF:

0.00

AC:

AN:

34052

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3108

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

929204

Other (OTH)

AF:

0.00

AC:

AN:

44202

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.011

BayesDel_noAF

Benign

-0.25

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.071

Eigen

Benign

-0.28

Eigen_PC

Benign

-0.14

FATHMM_MKL

Benign

0.43

LIST_S2

Benign

0.49

M_CAP

Uncertain

0.23

MetaRNN

Benign

0.16

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.69

PhyloP100

2.4

PrimateAI

Pathogenic

0.91

PROVEAN

Benign

-0.070

REVEL

Benign

0.098

Sift

Benign

0.061

Sift4G

Pathogenic

0.0

Polyphen

0.24

Vest4

0.36

MutPred

0.34

Loss of helix (P = 0.0068)

MVP

0.21

MPC

1.2

ClinPred

0.54

GERP RS

3.6

PromoterAI

-0.0029

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

Varity_R

0.053

gMVP

0.31

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over