NM_018042.5:c.1147+492C>T

Variant names:

• chr17-35419782-G-A
• rs722374
• NM_018042.5:c.1147+492C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018042.5(SLFN12):​c.1147+492C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,018 control chromosomes in the GnomAD database, including 4,360 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 0.19 (4360 hom., cov: 32)
• Consequence: SLFN12 NM_018042.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 4 publications found

Genes affected

SLFN12 (HGNC:25500): (schlafen family member 12) Predicted to act upstream of or within negative regulation of cell population proliferation. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLFN12	NM_018042.5	c.1147+492C>T		intron_variant	Intron 3 of 3	ENST00000304905.10	NP_060512.3
SLFN12	NM_001289009.2	c.1147+492C>T		intron_variant	Intron 3 of 3		NP_001275938.1
SLFN12	XM_005257995.6	c.1147+492C>T		intron_variant	Intron 4 of 4		XP_005258052.1
SLFN12	XM_024450822.2	c.1147+492C>T		intron_variant	Intron 5 of 5		XP_024306590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLFN12	ENST00000304905.10	c.1147+492C>T		intron_variant	Intron 3 of 3	1	NM_018042.5	ENSP00000302077.5

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29484 AN: 151900 Hom.: 4353 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0880

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.0530

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.0959

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.194 AC: 29537 AN: 152018 Hom.: 4360 Cov.: 32 AF XY: 0.195 AC XY: 14506 AN XY: 74322

African (AFR) AF: 0.410 AC: 16988 AN: 41444

American (AMR) AF: 0.162 AC: 2477 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3468

East Asian (EAS) AF: 0.0884 AC: 458 AN: 5182

South Asian (SAS) AF: 0.287 AC: 1384 AN: 4820

European-Finnish (FIN) AF: 0.0530 AC: 559 AN: 10550

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.0960 AC: 6523 AN: 67982

Other (OTH) AF: 0.180 AC: 379 AN: 2106

Alfa AF: 0.137 Hom.: 2509

Bravo AF: 0.209

Asia WGS AF: 0.198 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.80
PhyloP100		0.013
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs722374; hg19: chr17-33746801;