17-35516493-T-G

Position:

• chr17-35516493-T-G

Variant summary

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

The NM_001363830.2(SLFN12L):​c.86+5786A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,186 control chromosomes in the GnomAD database, including 39,668 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 0.72 (39668 hom., cov: 33)
• Consequence: SLFN12L NM_001363830.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

Genes affected

SLFN12L (HGNC:33920): (schlafen family member 12 like) Predicted to be integral component of 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLFN12L	NM_001363830.2	c.86+5786A>C		intron_variant		ENST00000628453.4	NP_001350759.2
SLFN12L	NM_001195790.3	c.-288+5786A>C		intron_variant			NP_001182719.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLFN12L	ENST00000628453.4	c.86+5786A>C		intron_variant		5	NM_001363830.2	ENSP00000487397	A2

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108918 AN: 152068 Hom.: 39662 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.716 AC: 108974 AN: 152186 Hom.: 39668 Cov.: 33 AF XY: 0.716 AC XY: 53259 AN XY: 74388

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.725

Alfa AF: 0.754 Hom.: 52941

Bravo AF: 0.709

Asia WGS AF: 0.649 AC: 2253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8070473; hg19: chr17-33843512;