chr5-172915596-C-T

Position:

• chr5-172915596-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The ENST00000326654.7(ERGIC1):​c.*518C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00255 in 471,210 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0025 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0026 (2 hom.)
• Consequence: ERGIC1 ENST00000326654.7 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.226

Genes affected

ERGIC1 (HGNC:29205): (endoplasmic reticulum-golgi intermediate compartment 1) This gene encodes a cycling membrane protein which is an endoplasmic reticulum-golgi intermediate compartment (ERGIC) protein which interacts with other members of this protein family to increase their turnover. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 5-172915596-C-T is Benign according to our data. Variant chr5-172915596-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2656080.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERGIC1	NM_001031711.3	c.375+758C>T		intron_variant		ENST00000393784.8	NP_001026881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERGIC1	ENST00000393784.8	c.375+758C>T		intron_variant		1	NM_001031711.3	ENSP00000377374	P1

Frequencies

GnomAD3 genomes AF: 0.00252 AC: 384 AN: 152216 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.000844

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.00131

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00122

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00420

Gnomad OTH AF: 0.00334

GnomAD3 exomes AF: 0.00234 AC: 348 AN: 148874 Hom.: 1 AF XY: 0.00231 AC XY: 185 AN XY: 80178

Gnomad AFR exome AF: 0.000444

Gnomad AMR exome AF: 0.00147

Gnomad ASJ exome AF: 0.00371

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00160

Gnomad FIN exome AF: 0.00132

Gnomad NFE exome AF: 0.00381

Gnomad OTH exome AF: 0.00255

GnomAD4 exome AF: 0.00256 AC: 817 AN: 318876 Hom.: 2 Cov.: 0 AF XY: 0.00241 AC XY: 435 AN XY: 180144

Gnomad4 AFR exome AF: 0.000811

Gnomad4 AMR exome AF: 0.00136

Gnomad4 ASJ exome AF: 0.00417

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00154

Gnomad4 FIN exome AF: 0.00163

Gnomad4 NFE exome AF: 0.00343

Gnomad4 OTH exome AF: 0.00286

GnomAD4 genome AF: 0.00252 AC: 384 AN: 152334 Hom.: 2 Cov.: 32 AF XY: 0.00252 AC XY: 188 AN XY: 74490

Gnomad4 AFR AF: 0.000842

Gnomad4 AMR AF: 0.00131

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00122

Gnomad4 NFE AF: 0.00420

Gnomad4 OTH AF: 0.00331

Alfa AF: 0.00310 Hom.: 1

Bravo AF: 0.00220

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

ERGIC1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.8
DANN	Benign	0.94

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: rs145748219; hg19: chr5-172342599;