NM_015187.5:c.1565-3722C>T

Variant names:

• chr4-25808474-G-A
• rs959903
• NM_015187.5:c.1565-3722C>T

Variant summary

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

The NM_015187.5(SEL1L3):​c.1565-3722C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,040 control chromosomes in the GnomAD database, including 5,239 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 0.25 (5239 hom., cov: 32)
• Consequence: SEL1L3 NM_015187.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEL1L3	NM_015187.5	c.1565-3722C>T		intron_variant	Intron 9 of 23	ENST00000399878.8	NP_056002.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEL1L3	ENST00000399878.8	c.1565-3722C>T		intron_variant	Intron 9 of 23	1	NM_015187.5	ENSP00000382767.3
SEL1L3	ENST00000264868.9	c.1460-3722C>T		intron_variant	Intron 9 of 23	1		ENSP00000264868.5
SEL1L3	ENST00000502949.5	c.1106-3722C>T		intron_variant	Intron 9 of 23	2		ENSP00000425438.1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38689 AN: 151922 Hom.: 5230 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.255 AC: 38725 AN: 152040 Hom.: 5239 Cov.: 32 AF XY: 0.254 AC XY: 18881 AN XY: 74296

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.260

Alfa AF: 0.278 Hom.: 10045

Bravo AF: 0.254

Asia WGS AF: 0.215 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.047
DANN	Benign	0.79

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: rs959903; hg19: chr4-25810096;