rs2794062

Variant names:

• chr1-148784552-A-G
• rs2794062
• ENST00000616023.1:n.43T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The ENST00000616023.1(SEC22B3P):​n.43T>C variant causes a non coding transcript exon change. 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: 0)
• Consequence: SEC22B3P ENST00000616023.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.85
• Publications: 19 publications found

Genes affected

SEC22B3P (HGNC:53891): (SEC22 homolog B3, pseudogene)

ENSG00000299543 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEC22B3P	NR_158170.1	n.158T>C		non_coding_transcript_exon_variant	Exon 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEC22B3P	ENST00000616023.1	n.43T>C		non_coding_transcript_exon_variant	Exon 1 of 4	6
ENSG00000299543	ENST00000764483.1	n.84T>C		non_coding_transcript_exon_variant	Exon 2 of 5

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD2 exomes AF: 0.499 AC: 108209 AN: 217046 AF XY: 0.498

Gnomad AFR exome AF: 0.499

Gnomad AMR exome AF: 0.498

Gnomad ASJ exome AF: 0.499

Gnomad EAS exome AF: 0.499

Gnomad FIN exome AF: 0.499

Gnomad NFE exome AF: 0.499

Gnomad OTH exome AF: 0.497

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	20
DANN	Benign	0.91
PhyloP100		6.9

Splicing

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

Other links and lift over

dbSNP: rs2794062; hg19: chr1-145103947;