10-102854593-C-T

Variant names:

• chr10-102854593-C-T
• rs3824754
• NM_001136200.2:c.141+166C>T

Variant summary

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

The NM_001136200.2(BORCS7):​c.141+166C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 813,246 control chromosomes in the GnomAD database, including 6,198 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 0.091 (980 hom., cov: 31)
  • Exomes 𝑓: 0.11 (5218 hom.)
• Consequence: BORCS7 NM_001136200.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BORCS7	NM_001136200.2	c.141+166C>T		intron_variant	Intron 1 of 4	ENST00000339834.10	NP_001129672.1
BORCS7	NM_144591.5	c.141+166C>T		intron_variant	Intron 1 of 5		NP_653192.2
BORCS7-ASMT	NR_037644.1	n.218+166C>T		intron_variant	Intron 1 of 14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BORCS7	ENST00000339834.10	c.141+166C>T		intron_variant	Intron 1 of 4	1	NM_001136200.2	ENSP00000342331.5
BORCS7-ASMT	ENST00000299353.6	n.141+166C>T		intron_variant	Intron 1 of 14	5		ENSP00000299353.5

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13834 AN: 151868 Hom.: 976 Cov.: 31

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0988

Gnomad OTH AF: 0.105

GnomAD4 exome AF: 0.106 AC: 70412 AN: 661260 Hom.: 5218 AF XY: 0.110 AC XY: 36561 AN XY: 332040

Gnomad4 AFR exome AF: 0.0147

Gnomad4 AMR exome AF: 0.168

Gnomad4 ASJ exome AF: 0.0841

Gnomad4 EAS exome AF: 0.311

Gnomad4 SAS exome AF: 0.202

Gnomad4 FIN exome AF: 0.0890

Gnomad4 NFE exome AF: 0.0877

Gnomad4 OTH exome AF: 0.107

GnomAD4 genome AF: 0.0911 AC: 13843 AN: 151986 Hom.: 980 Cov.: 31 AF XY: 0.0943 AC XY: 7003 AN XY: 74270

Gnomad4 AFR AF: 0.0209

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0821

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.0876

Gnomad4 NFE AF: 0.0988

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0896 Hom.: 396

Bravo AF: 0.0926

Asia WGS AF: 0.217 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3824754; hg19: chr10-104614350;