17-35513276-C-G

Position:

• chr17-35513276-C-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+9003G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,138 control chromosomes in the GnomAD database, including 49,198 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 0.80 (49198 hom., cov: 32)
• Consequence: SLFN12L NM_001363830.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLFN12L	NM_001363830.2	c.86+9003G>C		intron_variant		ENST00000628453.4	NP_001350759.2
SLFN12L	NM_001195790.3	c.-288+9003G>C		intron_variant			NP_001182719.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLFN12L	ENST00000628453.4	c.86+9003G>C		intron_variant		5	NM_001363830.2	ENSP00000487397.4

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122063 AN: 152018 Hom.: 49167 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.803 AC: 122150 AN: 152138 Hom.: 49198 Cov.: 32 AF XY: 0.805 AC XY: 59850 AN XY: 74370

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.828

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.785

Alfa AF: 0.779 Hom.: 2474

Bravo AF: 0.800

Asia WGS AF: 0.828 AC: 2877 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	2.2
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8068353; hg19: chr17-33840295;