chr6-8010464-T-G

Position:

• chr6-8010464-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.372+15903A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,864 control chromosomes in the GnomAD database, including 15,980 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 0.44 (15980 hom., cov: 31)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

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 = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.422+15903A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLOC1S5-TXNDC5	ENST00000439343.2	n.372+15903A>C		intron_variant		2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67386 AN: 151746 Hom.: 15966 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.444 AC: 67437 AN: 151864 Hom.: 15980 Cov.: 31 AF XY: 0.450 AC XY: 33407 AN XY: 74222

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.422

Alfa AF: 0.460 Hom.: 10240

Bravo AF: 0.439

Asia WGS AF: 0.597 AC: 2078 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	1.7
DANN	Benign	0.79

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: rs1002308; hg19: chr6-8010697;