17-35360397-C-T

Position:

• chr17-35360397-C-T

Variant summary

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

The NM_001376007.1(SLFN11):​c.1070-26G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,586,064 control chromosomes in the GnomAD database, including 66,354 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 0.37 (12499 hom., cov: 29)
  • Exomes 𝑓: 0.26 (53855 hom.)
• Consequence: SLFN11 NM_001376007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

Genes affected

SLFN11 (HGNC:26633): (schlafen family member 11) Enables tRNA binding activity. Involved in several processes, including defense response to virus; negative regulation of G1/S transition of mitotic cell cycle; and replication fork arrest. Located in cytosol; nucleoplasm; and site of DNA damage. [provided by Alliance of Genome Resources, Apr 2022]

SLFN11 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLFN11	NM_001376007.1	c.1070-26G>A		intron_variant		ENST00000685675.1	NP_001362936.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLFN11	ENST00000685675.1	c.1070-26G>A		intron_variant			NM_001376007.1	ENSP00000510787.1
SLFN11	ENST00000308377.8	c.1070-26G>A		intron_variant		1		ENSP00000312402.4
SLFN11	ENST00000394566.5	c.1070-26G>A		intron_variant		2		ENSP00000378067.1
SLFN11	ENST00000586099.1	n.227-26G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55595 AN: 150480 Hom.: 12477 Cov.: 29

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.330

GnomAD3 exomes AF: 0.320 AC: 74170 AN: 231654 Hom.: 13929 AF XY: 0.306 AC XY: 38354 AN XY: 125486

Gnomad AFR exome AF: 0.622

Gnomad AMR exome AF: 0.455

Gnomad ASJ exome AF: 0.202

Gnomad EAS exome AF: 0.494

Gnomad SAS exome AF: 0.337

Gnomad FIN exome AF: 0.290

Gnomad NFE exome AF: 0.227

Gnomad OTH exome AF: 0.286

GnomAD4 exome AF: 0.258 AC: 370171 AN: 1435464 Hom.: 53855 Cov.: 29 AF XY: 0.257 AC XY: 183750 AN XY: 713704

Gnomad4 AFR exome AF: 0.627

Gnomad4 AMR exome AF: 0.446

Gnomad4 ASJ exome AF: 0.203

Gnomad4 EAS exome AF: 0.492

Gnomad4 SAS exome AF: 0.329

Gnomad4 FIN exome AF: 0.289

Gnomad4 NFE exome AF: 0.225

Gnomad4 OTH exome AF: 0.284

GnomAD4 genome AF: 0.370 AC: 55664 AN: 150600 Hom.: 12499 Cov.: 29 AF XY: 0.374 AC XY: 27445 AN XY: 73438

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.332

Alfa AF: 0.248 Hom.: 10719

Bravo AF: 0.389

Asia WGS AF: 0.436 AC: 1515 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.1
DANN	Benign	0.75

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: rs938298; hg19: chr17-33687416; COSMIC: COSV57700729; COSMIC: COSV57700729;