rs11731086

chr4-25759784-A-G

Variant summary

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

The NM_015187.5(SEL1L3):c.2956-716T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,138 control chromosomes in the GnomAD database, including 11,511 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 (11504 hom., cov: 31)
  • Exomes 𝑓: 0.39 (7 hom.)
• Consequence: SEL1L3 NM_015187.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

Genes affected

SEL1L3 (HGNC:29108): (SEL1L family member 3) Located in nucleoplasm. [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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEL1L3	NM_015187.5	c.2956-716T>C		intron_variant		ENST00000399878.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEL1L3	ENST00000399878.8	c.2956-716T>C		intron_variant		1	NM_015187.5	P1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58601 AN: 151924 Hom.: 11478 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.397

GnomAD4 exome AF: 0.385 AC: 37 AN: 96 Hom.: 7 Cov.: 0 AF XY: 0.338 AC XY: 23 AN XY: 68

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.750

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.321

GnomAD4 genome AF: 0.386 AC: 58677 AN: 152042 Hom.: 11504 Cov.: 31 AF XY: 0.393 AC XY: 29195 AN XY: 74320

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.400

Alfa AF: 0.375 Hom.: 14358

Bravo AF: 0.391

Asia WGS AF: 0.399 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.17
Dann	Benign	0.34
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.97

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: rs11731086; hg19: chr4-25761406;