chr10-102856906-T-C

Position:

• chr10-102856906-T-C

Variant summary

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

The NM_001136200.2(BORCS7):​c.141+2479T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,164 control chromosomes in the GnomAD database, including 1,838 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 0.14 (1838 hom., cov: 31)
• Consequence: BORCS7 NM_001136200.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.39

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BORCS7	NM_001136200.2	c.141+2479T>C		intron_variant		ENST00000339834.10	NP_001129672.1
BORCS7	NM_144591.5	c.141+2479T>C		intron_variant			NP_653192.2
BORCS7-ASMT	NR_037644.1	n.218+2479T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BORCS7	ENST00000339834.10	c.141+2479T>C		intron_variant		1	NM_001136200.2	ENSP00000342331.5
BORCS7	ENST00000369883.3	c.141+2479T>C		intron_variant		1		ENSP00000358899.3
BORCS7-ASMT	ENST00000299353.6	n.141+2479T>C		intron_variant		5		ENSP00000299353.5
BORCS7	ENST00000478833.1	n.19+2479T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21600 AN: 152046 Hom.: 1821 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.0846

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.142 AC: 21657 AN: 152164 Hom.: 1838 Cov.: 31 AF XY: 0.142 AC XY: 10591 AN XY: 74398

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.0846

Gnomad4 NFE AF: 0.0993

Gnomad4 OTH AF: 0.142

Alfa AF: 0.116 Hom.: 622

Bravo AF: 0.152

Asia WGS AF: 0.220 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.60

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: rs4409766; hg19: chr10-104616663;