rs1838149

Variant names:

• chr17-35492283-G-A
• rs1838149
• NM_001363830.2:c.87-12088C>T

Variant summary

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

The NM_001363830.2(SLFN12L):​c.87-12088C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,958 control chromosomes in the GnomAD database, including 12,071 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 0.39 (12071 hom., cov: 31)
• Consequence: SLFN12L NM_001363830.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 8 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: 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 = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLFN12L	NM_001363830.2	c.87-12088C>T		intron_variant	Intron 2 of 4	ENST00000628453.4	NP_001350759.2
E2F3P1		n.35492283G>A		intragenic_variant
SLFN12L	NM_001195790.3	c.-287-4311C>T		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.87-12088C>T		intron_variant	Intron 2 of 4	5	NM_001363830.2	ENSP00000487397.4

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59461 AN: 151840 Hom.: 12074 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.0916

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.391 AC: 59486 AN: 151958 Hom.: 12071 Cov.: 31 AF XY: 0.383 AC XY: 28447 AN XY: 74266

African (AFR) AF: 0.433 AC: 17942 AN: 41432

American (AMR) AF: 0.342 AC: 5230 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3470

East Asian (EAS) AF: 0.0916 AC: 474 AN: 5176

South Asian (SAS) AF: 0.293 AC: 1412 AN: 4816

European-Finnish (FIN) AF: 0.320 AC: 3375 AN: 10548

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.416 AC: 28252 AN: 67930

Other (OTH) AF: 0.409 AC: 862 AN: 2108

Alfa AF: 0.403 Hom.: 1544

Bravo AF: 0.399

Asia WGS AF: 0.194 AC: 677 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	9.2
DANN	Benign	0.29
PhyloP100		0.042
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1838149; hg19: chr17-33819302; COSMIC: COSV53474226; COSMIC: COSV53474226;