rs1055636

Positions:

• chr17-35267301-A-C
• chr17-35267301-A-T

Variant summary

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

The NM_144975.4(SLFN5):​c.*1413A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,118 control chromosomes in the GnomAD database, including 10,021 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 0.33 (10021 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: SLFN5 NM_144975.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

SLFN5 (HGNC:28286): (schlafen family member 5) Predicted to enable ATP binding activity. Predicted to be involved in cell differentiation. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLFN5	NM_144975.4	c.*1413A>C		3_prime_UTR_variant	5/5	ENST00000299977.9	NP_659412.3
SLFN5	NM_001330183.2	c.*2198A>C		3_prime_UTR_variant	4/4		NP_001317112.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLFN5	ENST00000299977.9	c.*1413A>C		3_prime_UTR_variant	5/5	1	NM_144975.4	ENSP00000299977	P1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49795 AN: 151996 Hom.: 10025 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.0897

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.364

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.327 AC: 49786 AN: 152114 Hom.: 10021 Cov.: 32 AF XY: 0.323 AC XY: 24021 AN XY: 74342

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.0897

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.362

Alfa AF: 0.435 Hom.: 28839

Bravo AF: 0.308

Asia WGS AF: 0.190 AC: 662 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.9
DANN	Benign	0.88

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

Publications

LitVar

Other links and lift over

dbSNP: rs1055636; hg19: chr17-33594320;