NM_001136200.2:c.110A>G

Variant names:

• chr10-102854396-A-G
• NM_001136200.2:c.110A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001136200.2(BORCS7):​c.110A>G​(p.Lys37Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: BORCS7 NM_001136200.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.82
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.060058862).

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.110A>G	p.Lys37Arg	missense	Exon 1 of 5	NP_001129672.1	Q96B45
	BORCS7	NM_144591.5		c.110A>G	p.Lys37Arg	missense	Exon 1 of 6	NP_653192.2	Q96B45
	BORCS7-ASMT	NR_037644.1		n.187A>G		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.110A>G	p.Lys37Arg	missense	Exon 1 of 5	ENSP00000342331.5	Q96B45
	BORCS7	ENST00000369883.3	TSL:1	c.110A>G	p.Lys37Arg	missense	Exon 1 of 6	ENSP00000358899.3	Q96B45
	BORCS7-ASMT	ENST00000299353.6	TSL:5	n.110A>G		non_coding_transcript_exon	Exon 1 of 15	ENSP00000299353.5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.070
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	22
DANN	Benign	0.85
Eigen	Benign	-0.42
Eigen_PC	Benign	-0.15
FATHMM_MKL	Benign	0.64	D
LIST_S2	Benign	0.83	T
M_CAP	Benign	0.0034	T
MetaRNN	Benign	0.060	T
MetaSVM	Benign	-1.0	T
PhyloP100		5.8
PROVEAN	Benign	1.7	N
REVEL	Benign	0.053
Sift	Benign	1.0	T
Sift4G	Benign	0.92	T
Vest4		0.21
MVP		0.23
MPC		0.13
ClinPred		0.16	T
GERP RS		4.8
PromoterAI		-0.048	Neutral
gMVP		0.22
Mutation Taster		=78/22	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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

Other links and lift over

hg19: chr10-104614153;