rs3738369

Positions:

• chr1-41020736-G-A

Variant summary

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

The ENST00000302946.13(SLFNL1):​c.-76C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,398,696 control chromosomes in the GnomAD database, including 11,379 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 0.11 (1240 hom., cov: 32)
  • Exomes 𝑓: 0.12 (10139 hom.)
• Consequence: SLFNL1 ENST00000302946.13 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

Genes affected

SLFNL1 (HGNC:26313): (schlafen like 1) Predicted to enable ATP binding activity. [provided by Alliance of Genome Resources, Apr 2022]

SLFNL1-AS1 (HGNC:44126): (SLFNL1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLFNL1	NM_144990.4	c.-76C>T		5_prime_UTR_variant	3/6	ENST00000302946.13	NP_659427.3
SLFNL1-AS1	NR_037868.1	n.3812+2335G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLFNL1	ENST00000302946.13	c.-76C>T		5_prime_UTR_variant	3/6	1	NM_144990.4	ENSP00000304401	P2
SLFNL1-AS1	ENST00000626479.1	n.3812+2335G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16130 AN: 152020 Hom.: 1237 Cov.: 32

Gnomad AFR AF: 0.0301

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.120 AC: 149088 AN: 1246558 Hom.: 10139 Cov.: 17 AF XY: 0.119 AC XY: 73663 AN XY: 618512

Gnomad4 AFR exome AF: 0.0256

Gnomad4 AMR exome AF: 0.284

Gnomad4 ASJ exome AF: 0.114

Gnomad4 EAS exome AF: 0.270

Gnomad4 SAS exome AF: 0.113

Gnomad4 FIN exome AF: 0.107

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.130

GnomAD4 genome AF: 0.106 AC: 16139 AN: 152138 Hom.: 1240 Cov.: 32 AF XY: 0.110 AC XY: 8171 AN XY: 74372

Gnomad4 AFR AF: 0.0300

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.125

Alfa AF: 0.114 Hom.: 1086

Bravo AF: 0.113

Asia WGS AF: 0.172 AC: 595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3738369; hg19: chr1-41486408; COSMIC: COSV57235990;