rs9916629

chr17-35469241-T-C

Variant summary

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

The NM_001363830.2(SLFN12L):c.*5682A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 147,414 control chromosomes in the GnomAD database, including 7,351 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 0.31 (7351 hom., cov: 23)
• Consequence: SLFN12L NM_001363830.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLFN12L	NM_001363830.2	c.*5682A>G		3_prime_UTR_variant	5/5	ENST00000628453.4
SLFN12L	NM_001195790.3	c.*5682A>G		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLFN12L	ENST00000628453.4	c.*5682A>G		3_prime_UTR_variant	5/5	5	NM_001363830.2	A2
SLFN12L	ENST00000260908.13	c.*5682A>G		3_prime_UTR_variant	4/4	5		P2
SLFN12L	ENST00000587436.1	n.396-4579A>G		intron_variant, non_coding_transcript_variant		2
SLFN12L	ENST00000590802.1	n.153-4660A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.311 AC: 45762 AN: 147358 Hom.: 7344 Cov.: 23

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.390

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.311 AC: 45778 AN: 147414 Hom.: 7351 Cov.: 23 AF XY: 0.303 AC XY: 21737 AN XY: 71758

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.0943

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.327

Alfa AF: 0.322 Hom.: 7818

Bravo AF: 0.319

Asia WGS AF: 0.155 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.4
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9916629; hg19: chr17-33796260;