chr6-7913313-A-G

Position:

• chr6-7913313-A-G

Variant summary

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

The ENST00000439343.2(BLOC1S5-TXNDC5):​n.373-8590T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,146 control chromosomes in the GnomAD database, including 1,161 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 0.11 (1161 hom., cov: 32)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.423-8590T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLOC1S5-TXNDC5	ENST00000439343.2	n.373-8590T>C		intron_variant		2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17077 AN: 152028 Hom.: 1165 Cov.: 32

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0567

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.112 AC: 17080 AN: 152146 Hom.: 1161 Cov.: 32 AF XY: 0.112 AC XY: 8356 AN XY: 74382

Gnomad4 AFR AF: 0.0841

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0567

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.132

Alfa AF: 0.121 Hom.: 794

Bravo AF: 0.122

Asia WGS AF: 0.199 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.72
DANN	Benign	0.73

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: rs1632346; hg19: chr6-7913546;