chr17-35519585-G-A

Variant names:

• chr17-35519585-G-A
• rs4796093
• NM_001363830.2:c.86+2694C>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.86+2694C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,982 control chromosomes in the GnomAD database, including 33,516 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 0.65 (33516 hom., cov: 31)
• Consequence: SLFN12L NM_001363830.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLFN12L	NM_001363830.2	c.86+2694C>T		intron_variant	Intron 2 of 4	ENST00000628453.4	NP_001350759.2
SLFN12L	NM_001195790.3	c.-288+2694C>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.86+2694C>T		intron_variant	Intron 2 of 4	5	NM_001363830.2	ENSP00000487397.4
SLFN12L	ENST00000714259.1	n.802+2694C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98201 AN: 151862 Hom.: 33521 Cov.: 31

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.646 AC: 98217 AN: 151982 Hom.: 33516 Cov.: 31 AF XY: 0.648 AC XY: 48141 AN XY: 74278

African (AFR) AF: 0.420 AC: 17389 AN: 41400

American (AMR) AF: 0.741 AC: 11323 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2144 AN: 3472

East Asian (EAS) AF: 0.546 AC: 2825 AN: 5170

South Asian (SAS) AF: 0.614 AC: 2956 AN: 4816

European-Finnish (FIN) AF: 0.790 AC: 8347 AN: 10562

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50870 AN: 67970

Other (OTH) AF: 0.659 AC: 1389 AN: 2108

Alfa AF: 0.706 Hom.: 120757

Bravo AF: 0.634

Asia WGS AF: 0.570 AC: 1981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.65
PhyloP100		0.25
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: rs4796093; hg19: chr17-33846604;