16-2209404-GC-AG

Variant names:

• chr16-2209404-GC-AG
• NM_182563.4:c.644_645delGCinsCT
• BRICD5 p.Ser215Thr

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_182563.4(BRICD5):​c.644_645delGCinsCT​(p.Ser215Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S215C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 34)
• Consequence: BRICD5 NM_182563.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.63
• Publications: 0 publications found

Genes affected

BRICD5 (HGNC:28309): (BRICHOS domain containing 5) Predicted to be involved in regulation of cell population proliferation. Predicted to be integral component of membrane. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

MLST8 (HGNC:24825): (MTOR associated protein, LST8 homolog) Enables protein serine/threonine kinase activator activity. Involved in TORC1 signaling; positive regulation of TOR signaling; and regulation of actin cytoskeleton organization. Part of TORC1 complex and TORC2 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182563.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRICD5	NM_182563.4	MANE Select	c.644_645delGCinsCT	p.Ser215Thr	missense	N/A	NP_872369.2	Q6PL45-2
	MLST8	NM_022372.6	MANE Select	c.*527_*528delGCinsAG		3_prime_UTR	Exon 9 of 9	NP_071767.3
	MLST8	NM_001352057.2		c.*527_*528delGCinsAG		3_prime_UTR	Exon 9 of 9	NP_001338986.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRICD5	ENST00000328540.8	TSL:1 MANE Select	c.644_645delGCinsCT	p.Ser215Thr	missense	N/A	ENSP00000332389.3	Q6PL45-2
	MLST8	ENST00000569417.6	TSL:1 MANE Select	c.*527_*528delGCinsAG		3_prime_UTR	Exon 9 of 9	ENSP00000456405.1	Q9BVC4-1
	MLST8	ENST00000301724.14	TSL:1	c.*669_*670delGCinsAG		3_prime_UTR	Exon 8 of 8	ENSP00000301724.10	A0A0A0MR05

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr16-2259405;