6-107868223-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_007214.5(SEC63):c.*3480del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.94 (64646 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: SEC63 NM_007214.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00

Genes affected

SEC63 (HGNC:21082): (SEC63 homolog, protein translocation regulator) The Sec61 complex is the central component of the protein translocation apparatus of the endoplasmic reticulum (ER) membrane. The protein encoded by this gene and SEC62 protein are found to be associated with ribosome-free SEC61 complex. It is speculated that Sec61-Sec62-Sec63 may perform post-translational protein translocation into the ER. The Sec61-Sec62-Sec63 complex might also perform the backward transport of ER proteins that are subject to the ubiquitin-proteasome-dependent degradation pathway. The encoded protein is an integral membrane protein located in the rough ER. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-107868223-TA-T is Benign according to our data. Variant chr6-107868223-TA-T is described in ClinVar as [Benign]. Clinvar id is 354821.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEC63	NM_007214.5	c.*3480del		3_prime_UTR_variant	21/21	ENST00000369002.9
SEC63	XM_047418130.1	c.*3480del		3_prime_UTR_variant	21/21
SEC63	XM_047418131.1	c.*3480del		3_prime_UTR_variant	20/20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEC63	ENST00000369002.9	c.*3480del		3_prime_UTR_variant	21/21	1	NM_007214.5	P1

Frequencies

GnomAD3 genomes AF: 0.942 AC: 136940 AN: 145352 Hom.: 64623 Cov.: 0

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.977

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.948

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.942 AC: 137000 AN: 145426 Hom.: 64646 Cov.: 0 AF XY: 0.940 AC XY: 66222 AN XY: 70474

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.973

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.955

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.950

Gnomad4 OTH AF: 0.947

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Polycystic liver disease 1 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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: rs56104837; hg19: chr6-108189427;