rs7098825

Variant names:

• chr10-102868477-T-C
• rs7098825
• ENST00000299353.6:n.*9-1328T>C

Variant summary

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

The ENST00000299353.6(BORCS7-ASMT):​n.*9-1328T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,116 control chromosomes in the GnomAD database, including 1,124 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 0.11 (1124 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: BORCS7-ASMT ENST00000299353.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 20 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]

U6 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902567		n.102868477T>C		intragenic_variant
BORCS7-ASMT	NR_037644.1	n.407-1328T>C		intron_variant	Intron 5 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BORCS7-ASMT	ENST00000299353.6	n.*9-1328T>C		intron_variant	Intron 5 of 14	5		ENSP00000299353.5
U6	ENST00000636230.1	n.57T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000296999	ENST00000744161.1	n.88-1844A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16690 AN: 151998 Hom.: 1117 Cov.: 32

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0799

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.117

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.110 AC: 16715 AN: 152116 Hom.: 1124 Cov.: 32 AF XY: 0.112 AC XY: 8298 AN XY: 74370

African (AFR) AF: 0.0816 AC: 3386 AN: 41484

American (AMR) AF: 0.149 AC: 2268 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0799 AC: 277 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1536 AN: 5172

South Asian (SAS) AF: 0.191 AC: 920 AN: 4818

European-Finnish (FIN) AF: 0.0951 AC: 1007 AN: 10594

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7018 AN: 67994

Other (OTH) AF: 0.120 AC: 253 AN: 2108

Alfa AF: 0.102 Hom.: 147

Bravo AF: 0.113

Asia WGS AF: 0.211 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		-0.61

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

Other links and lift over

dbSNP: rs7098825; hg19: chr10-104628234;