chr10-102869116-A-G

Variant names:

• chr10-102869116-A-G
• rs7085104
• ENST00000299353.6:n.*9-689A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000299353.6(BORCS7-ASMT):​n.*9-689A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,092 control chromosomes in the GnomAD database, including 9,796 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 0.35 (9796 hom., cov: 32)
• Consequence: BORCS7-ASMT ENST00000299353.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600
• Publications: 93 publications found

Genes affected

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]

ENSG00000296999 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000299353.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BORCS7-ASMT	NR_037644.1		n.407-689A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BORCS7-ASMT	ENST00000299353.6	TSL:5	n.*9-689A>G		intron	N/A	ENSP00000299353.5
	ENSG00000296999	ENST00000744161.1		n.87+1706T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53935 AN: 151974 Hom.: 9788 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.355 AC: 53982 AN: 152092 Hom.: 9796 Cov.: 32 AF XY: 0.353 AC XY: 26243 AN XY: 74346

African (AFR) AF: 0.347 AC: 14423 AN: 41506

American (AMR) AF: 0.370 AC: 5653 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3470

East Asian (EAS) AF: 0.513 AC: 2651 AN: 5168

South Asian (SAS) AF: 0.316 AC: 1522 AN: 4822

European-Finnish (FIN) AF: 0.307 AC: 3243 AN: 10564

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24141 AN: 67976

Other (OTH) AF: 0.368 AC: 776 AN: 2110

Alfa AF: 0.357 Hom.: 42133

Bravo AF: 0.362

Asia WGS AF: 0.374 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.68
PhyloP100		-0.060
PromoterAI		-0.084	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs7085104; hg19: chr10-104628873;