rs1265247333

Variant names:

• chr17-35440845-G-A
• rs1265247333
• NM_144682.6:c.2444C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-35440845-G-A
• chr17-35440845-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_144682.6(SLFN13):​c.2444C>T​(p.Thr815Ile) 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. 14/22 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. T815N) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLFN13 NM_144682.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 1 publications found

Genes affected

SLFN13 (HGNC:26481): (schlafen family member 13) Enables endoribonuclease activity. Involved in rRNA catabolic process and tRNA catabolic process. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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=0.10372272).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLFN13	NM_144682.6	c.2444C>T	p.Thr815Ile	missense_variant	Exon 6 of 6	ENST00000285013.11	NP_653283.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLFN13	ENST00000285013.11	c.2444C>T	p.Thr815Ile	missense_variant	Exon 6 of 6	1	NM_144682.6	ENSP00000285013.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.41
BayesDel_addAF	Benign	-0.053	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	3.2
DANN	Benign	0.95
DEOGEN2	Benign	0.026	T;T;T;.;T
Eigen	Benign	-0.84
Eigen_PC	Benign	-0.99
FATHMM_MKL	Benign	0.026	N
LIST_S2	Benign	0.58	.;.;T;T;.
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.10	T;T;T;T;T
MetaSVM	Benign	-0.46	T
MutationAssessor	Uncertain	2.1	M;M;M;.;M
PhyloP100		-0.50
PrimateAI	Benign	0.48	T
PROVEAN	Uncertain	-3.7	D;D;D;D;.
REVEL	Benign	0.23
Sift	Benign	0.058	T;T;T;T;.
Sift4G	Uncertain	0.060	T;T;T;T;T
Polyphen		0.096	B;B;B;B;B
Vest4		0.092
MutPred		0.39		Gain of helix (P = 0.0199);Gain of helix (P = 0.0199);Gain of helix (P = 0.0199);.;Gain of helix (P = 0.0199);
MVP		0.54
MPC		0.098
ClinPred		0.32	T
GERP RS		-0.54
Varity_R		0.091
gMVP		0.28

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: rs1265247333; hg19: chr17-33767864;