rs10484327

Positions:

• chr6-7942333-T-G

Variant summary

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

The ENST00000439343.2(BLOC1S5-TXNDC5):​n.373-37610A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0572 in 152,324 control chromosomes in the GnomAD database, including 355 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 0.057 (355 hom., cov: 32)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

Genes affected

BLOC1S5-TXNDC5 (HGNC:42001): (BLOC1S5-TXNDC5 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring MUTED (muted homolog) and TXNDC5 (thioredoxin domain containing 5) genes on chromosome 6. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is unlikely to produce a protein product. [provided by RefSeq, Dec 2010]

BLOC1S5-TXNDC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.423-37610A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLOC1S5-TXNDC5	ENST00000439343.2	n.373-37610A>C		intron_variant		2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.0572 AC: 8709 AN: 152206 Hom.: 356 Cov.: 32

Gnomad AFR AF: 0.0173

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.0863

Gnomad SAS AF: 0.0960

Gnomad FIN AF: 0.0310

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0763

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0572 AC: 8712 AN: 152324 Hom.: 355 Cov.: 32 AF XY: 0.0574 AC XY: 4274 AN XY: 74496

Gnomad4 AFR AF: 0.0174

Gnomad4 AMR AF: 0.0778

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.0864

Gnomad4 SAS AF: 0.0959

Gnomad4 FIN AF: 0.0310

Gnomad4 NFE AF: 0.0763

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0710 Hom.: 220

Bravo AF: 0.0591

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.77

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: rs10484327; hg19: chr6-7942566;