16-23445969-TAAAAAA-TAAA

Variant names:

• chr16-23445969-TAAA-T
• rs71379679
• NM_153603.4:c.170-11_170-9delTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2 BP6_Moderate BS1

The NM_153603.4(COG7):​c.170-11_170-9delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0027 in 1,471,896 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00012 (0 hom., cov: 25)
  • Exomes 𝑓: 0.0029 (0 hom.)
• Consequence: COG7 NM_153603.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.874

Genes affected

COG7 (HGNC:18622): (component of oligomeric golgi complex 7) The protein encoded by this gene resides in the golgi, and constitutes one of the 8 subunits of the conserved oligomeric Golgi (COG) complex, which is required for normal golgi morphology and localization. Mutations in this gene are associated with the congenital disorder of glycosylation type IIe.[provided by RefSeq, May 2010]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 16-23445969-TAAA-T is Benign according to our data. Variant chr16-23445969-TAAA-T is described in ClinVar as [Benign]. Clinvar id is 235231.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00295 (3955/1342692) while in subpopulation AMR AF= 0.00594 (226/38068). AF 95% confidence interval is 0.0053. There are 0 homozygotes in gnomad4_exome. There are 1945 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COG7	NM_153603.4	c.170-11_170-9delTTT		intron_variant	Intron 1 of 16	ENST00000307149.10	NP_705831.1
COG7	XM_017023870.2	c.-26-11_-26-9delTTT		intron_variant	Intron 1 of 16		XP_016879359.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COG7	ENST00000307149.10	c.170-11_170-9delTTT		intron_variant	Intron 1 of 16	1	NM_153603.4	ENSP00000305442.5

Frequencies

GnomAD3 genomes AF: 0.000116 AC: 15 AN: 129204 Hom.: 0 Cov.: 25

Gnomad AFR AF: 0.0000286

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000159

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000562

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000117

Gnomad OTH AF: 0.000575

GnomAD4 exome AF: 0.00295 AC: 3955 AN: 1342692 Hom.: 0 AF XY: 0.00291 AC XY: 1945 AN XY: 669258

Gnomad4 AFR exome AF: 0.00400

Gnomad4 AMR exome AF: 0.00594

Gnomad4 ASJ exome AF: 0.00264

Gnomad4 EAS exome AF: 0.00476

Gnomad4 SAS exome AF: 0.00313

Gnomad4 FIN exome AF: 0.00562

Gnomad4 NFE exome AF: 0.00259

Gnomad4 OTH exome AF: 0.00373

GnomAD4 genome AF: 0.000116 AC: 15 AN: 129204 Hom.: 0 Cov.: 25 AF XY: 0.000177 AC XY: 11 AN XY: 62150

Gnomad4 AFR AF: 0.0000286

Gnomad4 AMR AF: 0.000159

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000562

Gnomad4 NFE AF: 0.000117

Gnomad4 OTH AF: 0.000575

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 29, 2015

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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: rs71379679; hg19: chr16-23457290;