rs9916629

Variant names:

• chr17-35469241-T-C
• rs9916629
• NM_001363830.2:c.*5682A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLFN12L	NM_001363830.2	c.*5682A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000628453.4	NP_001350759.2
SLFN12L	NM_001195790.3	c.*5682A>G		3_prime_UTR_variant	Exon 6 of 6		NP_001182719.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLFN12L	ENST00000628453.4	c.*5682A>G		3_prime_UTR_variant	Exon 5 of 5	5	NM_001363830.2	ENSP00000487397.4
SLFN12L	ENST00000260908.13	c.*5682A>G		3_prime_UTR_variant	Exon 4 of 4	5		ENSP00000437635.2
SLFN12L	ENST00000587436.1	n.396-4579A>G		intron_variant	Intron 1 of 1	2
SLFN12L	ENST00000590802.1	n.153-4660A>G		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.335 AC: 13321 AN: 39732

American (AMR) AF: 0.282 AC: 4143 AN: 14674

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1326 AN: 3438

East Asian (EAS) AF: 0.0943 AC: 482 AN: 5110

South Asian (SAS) AF: 0.196 AC: 912 AN: 4658

European-Finnish (FIN) AF: 0.249 AC: 2347 AN: 9420

Middle Eastern (MID) AF: 0.408 AC: 115 AN: 282

European-Non Finnish (NFE) AF: 0.330 AC: 22161 AN: 67214

Other (OTH) AF: 0.327 AC: 649 AN: 1984

Alfa AF: 0.325 Hom.: 12922

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
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs9916629; hg19: chr17-33796260;