10-102854593-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 28 publications found

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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0147 AC: 238 AN: 16232

American (AMR) AF: 0.168 AC: 2849 AN: 16950

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 1215 AN: 14440

East Asian (EAS) AF: 0.311 AC: 9214 AN: 29652

South Asian (SAS) AF: 0.202 AC: 8830 AN: 43814

European-Finnish (FIN) AF: 0.0890 AC: 2545 AN: 28602

Middle Eastern (MID) AF: 0.0931 AC: 218 AN: 2342

European-Non Finnish (NFE) AF: 0.0877 AC: 41830 AN: 476916

Other (OTH) AF: 0.107 AC: 3473 AN: 32312

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

African (AFR) AF: 0.0209 AC: 866 AN: 41464

American (AMR) AF: 0.140 AC: 2129 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0821 AC: 285 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1724 AN: 5166

South Asian (SAS) AF: 0.194 AC: 933 AN: 4814

European-Finnish (FIN) AF: 0.0876 AC: 923 AN: 10536

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0988 AC: 6719 AN: 67984

Other (OTH) AF: 0.108 AC: 228 AN: 2102

Alfa AF: 0.0898 Hom.: 436

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
PhyloP100		-0.32
PromoterAI		-0.046	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3824754; hg19: chr10-104614350;