rs9909601

Variant names:

• chr17-35490403-A-C
• rs9909601
• NM_001363830.2:c.87-10208T>G

Your query was ambiguous. Multiple possible variants found:

• chr17-35490403-A-C
• chr17-35490403-A-G
• chr17-35490403-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001363830.2(SLFN12L):​c.87-10208T>G variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLFN12L NM_001363830.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 10 publications found

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]

E2F3P1 (HGNC:3116): (E2F transcription factor 3 pseudogene 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLFN12L	NM_001363830.2	c.87-10208T>G		intron_variant	Intron 2 of 4	ENST00000628453.4	NP_001350759.2
E2F3P1		n.35490403A>C		intragenic_variant
SLFN12L	NM_001195790.3	c.-287-2431T>G		intron_variant	Intron 2 of 5		NP_001182719.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLFN12L	ENST00000628453.4	c.87-10208T>G		intron_variant	Intron 2 of 4	5	NM_001363830.2	ENSP00000487397.4
E2F3P1	ENST00000589887.1	n.395A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1104070 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 564204

African (AFR) AF: 0.00 AC: 0 AN: 27738

American (AMR) AF: 0.00 AC: 0 AN: 44054

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24020

East Asian (EAS) AF: 0.00 AC: 0 AN: 37932

South Asian (SAS) AF: 0.00 AC: 0 AN: 79486

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52146

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5154

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 785060

Other (OTH) AF: 0.00 AC: 0 AN: 48480

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.67
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs9909601; hg19: chr17-33817422;