rs767070482

Variant names:

• chr10-102854366-C-T
• rs767070482
• NM_001136200.2:c.80C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-102854366-C-T
• chr10-102854366-C-A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001136200.2(BORCS7):​c.80C>T​(p.Thr27Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000117 in 1,578,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000099 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00012 (0 hom.)
• Consequence: BORCS7 NM_001136200.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.31
• Publications: 1 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.

• BP4: Computational evidence support a benign effect (MetaRNN=0.13305357).

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.80C>T	p.Thr27Ile	missense	Exon 1 of 5	NP_001129672.1	Q96B45
	BORCS7	NM_144591.5		c.80C>T	p.Thr27Ile	missense	Exon 1 of 6	NP_653192.2	Q96B45
	BORCS7-ASMT	NR_037644.1		n.157C>T		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.80C>T	p.Thr27Ile	missense	Exon 1 of 5	ENSP00000342331.5	Q96B45
	BORCS7	ENST00000369883.3	TSL:1	c.80C>T	p.Thr27Ile	missense	Exon 1 of 6	ENSP00000358899.3	Q96B45
	BORCS7-ASMT	ENST00000299353.6	TSL:5	n.80C>T		non_coding_transcript_exon	Exon 1 of 15	ENSP00000299353.5

Frequencies

GnomAD3 genomes AF: 0.0000986 AC: 15 AN: 152056 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000459

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000735

Gnomad OTH AF: 0.000961

GnomAD2 exomes AF: 0.000129 AC: 25 AN: 193262 AF XY: 0.0000876

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000327

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000134

Gnomad OTH exome AF: 0.000197

GnomAD4 exome AF: 0.000119 AC: 170 AN: 1426560 Hom.: 0 Cov.: 30 AF XY: 0.000105 AC XY: 74 AN XY: 705960

African (AFR) AF: 0.0000906 AC: 3 AN: 33106

American (AMR) AF: 0.000284 AC: 11 AN: 38798

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25404

East Asian (EAS) AF: 0.00 AC: 0 AN: 38600

South Asian (SAS) AF: 0.0000980 AC: 8 AN: 81618

European-Finnish (FIN) AF: 0.0000197 AC: 1 AN: 50770

Middle Eastern (MID) AF: 0.00385 AC: 22 AN: 5714

European-Non Finnish (NFE) AF: 0.000103 AC: 113 AN: 1093372

Other (OTH) AF: 0.000203 AC: 12 AN: 59178

GnomAD4 genome AF: 0.0000986 AC: 15 AN: 152056 Hom.: 0 Cov.: 31 AF XY: 0.0000943 AC XY: 7 AN XY: 74262

African (AFR) AF: 0.00 AC: 0 AN: 41400

American (AMR) AF: 0.000459 AC: 7 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5152

South Asian (SAS) AF: 0.00 AC: 0 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10600

Middle Eastern (MID) AF: 0.00316 AC: 1 AN: 316

European-Non Finnish (NFE) AF: 0.0000735 AC: 5 AN: 68032

Other (OTH) AF: 0.000961 AC: 2 AN: 2082

Alfa AF: 0.000183 Hom.: 0

Bravo AF: 0.000151

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000519 AC: 2

ExAC AF: 0.0000834 AC: 10

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	0.15
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.32
CADD	Uncertain	26
DANN	Uncertain	0.99
Eigen	Benign	0.051
Eigen_PC	Uncertain	0.25
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Benign	0.80	T
M_CAP	Benign	0.0036	T
MetaRNN	Benign	0.13	T
MetaSVM	Benign	-0.87	T
PhyloP100		5.3
PROVEAN	Benign	-0.44	N
REVEL	Benign	0.049
Sift	Benign	0.079	T
Sift4G	Benign	0.068	T
Vest4		0.36
MVP		0.46
MPC		0.18
ClinPred		0.11	T
GERP RS		5.9
PromoterAI		0.089	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6
gMVP		0.27
Mutation Taster		=61/39	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

dbSNP: rs767070482; hg19: chr10-104614123;