rs9527

Positions:

• chr10-102863821-C-T

Variant summary

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

The NM_001136200.2(BORCS7):​c.*897C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,170 control chromosomes in the GnomAD database, including 3,542 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 0.21 (3542 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: BORCS7 NM_001136200.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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]

BORCS7-ASMT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BORCS7	NM_001136200.2	c.*897C>T		3_prime_UTR_variant	5/5	ENST00000339834.10	NP_001129672.1
BORCS7	NM_144591.5	c.*100C>T		3_prime_UTR_variant	6/6		NP_653192.2
BORCS7-ASMT	NR_037644.1	n.406+889C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BORCS7	ENST00000339834.10	c.*897C>T		3_prime_UTR_variant	5/5	1	NM_001136200.2	ENSP00000342331.5
BORCS7	ENST00000369883.3	c.*100C>T		3_prime_UTR_variant	6/6	1		ENSP00000358899.3
BORCS7-ASMT	ENST00000299353.6	n.*8+889C>T		intron_variant		5		ENSP00000299353.5

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31974 AN: 152050 Hom.: 3542 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.224

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

GnomAD4 genome AF: 0.210 AC: 31977 AN: 152168 Hom.: 3542 Cov.: 32 AF XY: 0.207 AC XY: 15383 AN XY: 74396

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.223

Alfa AF: 0.241 Hom.: 6613

Bravo AF: 0.210

Asia WGS AF: 0.121 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.68

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: rs9527; hg19: chr10-104623578;