10-102858938-A-G

Variant names:

• chr10-102858938-A-G
• rs7096169
• NM_001136200.2:c.142-1394A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136200.2(BORCS7):​c.142-1394A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 151,234 control chromosomes in the GnomAD database, including 9,954 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (9954 hom., cov: 28)
• Consequence: BORCS7 NM_001136200.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BORCS7	NM_001136200.2	c.142-1394A>G		intron_variant	Intron 1 of 4	ENST00000339834.10	NP_001129672.1
BORCS7	NM_144591.5	c.142-1394A>G		intron_variant	Intron 1 of 5		NP_653192.2
BORCS7-ASMT	NR_037644.1	n.219-1394A>G		intron_variant	Intron 1 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BORCS7	ENST00000339834.10	c.142-1394A>G		intron_variant	Intron 1 of 4	1	NM_001136200.2	ENSP00000342331.5
BORCS7	ENST00000369883.3	c.142-1394A>G		intron_variant	Intron 1 of 5	1		ENSP00000358899.3
BORCS7-ASMT	ENST00000299353.6	n.142-1394A>G		intron_variant	Intron 1 of 14	5		ENSP00000299353.5
BORCS7	ENST00000478833.1	n.20-1394A>G		intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54343 AN: 151118 Hom.: 9936 Cov.: 28

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.360 AC: 54407 AN: 151234 Hom.: 9954 Cov.: 28 AF XY: 0.357 AC XY: 26384 AN XY: 73826

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.373

Alfa AF: 0.352 Hom.: 20623

Bravo AF: 0.367

Asia WGS AF: 0.378 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.64
DANN	Benign	0.56

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: rs7096169; hg19: chr10-104618695;