10-102854366-CC-AT

Variant names:

• chr10-102854366-CC-AT
• NM_001136200.2:c.80_81delCCinsAT
• BORCS7 p.Thr27Asn

Variant summary

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

The NM_001136200.2(BORCS7):​c.80_81delCCinsAT​(p.Thr27Asn) 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. T27I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: BORCS7 NM_001136200.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.31
• Publications: 0 publications found

Genes affected

BORCS7 (HGNC:23516): (BLOC-1 related complex subunit 7) Part of BORC complex. [provided by Alliance of Genome Resources, Apr 2022]

BORCS7-ASMT (HGNC:49183): (BORCS7-ASMT readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring C10orf32 (chromosome 10 open reading frame 32) and AS3MT (arsenic, +3 oxidation state, methyltransferase) genes. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is therefore unlikely to produce a protein product. [provided by RefSeq, Dec 2010]

ENSG00000282772 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136200.2. 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
	BORCS7	NM_001136200.2	MANE Select	c.80_81delCCinsAT	p.Thr27Asn	missense	N/A	NP_001129672.1	Q96B45
	BORCS7	NM_144591.5		c.80_81delCCinsAT	p.Thr27Asn	missense	N/A	NP_653192.2	Q96B45
	BORCS7-ASMT	NR_037644.1		n.157_158delCCinsAT		non_coding_transcript_exon	Exon 1 of 15

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BORCS7	ENST00000339834.10	TSL:1 MANE Select	c.80_81delCCinsAT	p.Thr27Asn	missense	N/A	ENSP00000342331.5	Q96B45
	BORCS7	ENST00000369883.3	TSL:1	c.80_81delCCinsAT	p.Thr27Asn	missense	N/A	ENSP00000358899.3	Q96B45
	BORCS7-ASMT	ENST00000299353.6	TSL:5	n.80_81delCCinsAT		non_coding_transcript_exon	Exon 1 of 15	ENSP00000299353.5

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.3

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: chr10-104614123;