ENST00000486903.5:n.-279+1909A>G

Variant names:

• chr20-13993703-T-C
• ENST00000486903.5:n.-279+1320A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000486903.5(SEL1L2):​n.-279+1320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SEL1L2 ENST00000486903.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.962
• Publications: 0 publications found

Genes affected

SEL1L2 (HGNC:15897): (SEL1L2 adaptor subunit of SYVN1 ubiquitin ligase) Predicted to contribute to ubiquitin-protein transferase activity. Predicted to be involved in ubiquitin-dependent ERAD pathway. Predicted to be integral component of membrane. Predicted to be part of Hrd1p ubiquitin ligase ERAD-L complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEL1L2	NM_001363752.2	c.-279+1320A>G		intron_variant	Intron 1 of 16		NP_001350681.1
SEL1L2	NR_073207.2	n.311+1320A>G		intron_variant	Intron 1 of 18
SEL1L2	XM_047440521.1	c.-279+1320A>G		intron_variant	Intron 1 of 19		XP_047296477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEL1L2	ENST00000486903.5	n.-279+1320A>G		intron_variant	Intron 1 of 18	1		ENSP00000493577.1
SEL1L2	ENST00000646153.1	c.-279+1320A>G		intron_variant	Intron 1 of 16			ENSP00000494947.1
SEL1L2	ENST00000473203.1	c.-279+2617A>G		intron_variant	Intron 1 of 4	4		ENSP00000420372.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.77
PhyloP100		0.96

Splicing

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

Other links and lift over

hg19: chr20-13974349;