6-7967713-C-T

Variant names:

• chr6-7967713-C-T
• rs1150893
• ENST00000439343.2:n.372+58654G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439343.2(BLOC1S5-TXNDC5):​n.372+58654G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 152,014 control chromosomes in the GnomAD database, including 21,313 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 0.52 (21313 hom., cov: 31)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 8 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.422+58654G>A		intron_variant	Intron 4 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLOC1S5-TXNDC5	ENST00000439343.2	n.372+58654G>A		intron_variant	Intron 4 of 12	2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79330 AN: 151896 Hom.: 21285 Cov.: 31

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.522 AC: 79403 AN: 152014 Hom.: 21313 Cov.: 31 AF XY: 0.529 AC XY: 39290 AN XY: 74282

African (AFR) AF: 0.427 AC: 17695 AN: 41434

American (AMR) AF: 0.577 AC: 8828 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1531 AN: 3468

East Asian (EAS) AF: 0.786 AC: 4061 AN: 5164

South Asian (SAS) AF: 0.560 AC: 2695 AN: 4810

European-Finnish (FIN) AF: 0.633 AC: 6698 AN: 10574

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36343 AN: 67968

Other (OTH) AF: 0.483 AC: 1016 AN: 2102

Alfa AF: 0.517 Hom.: 40130

Bravo AF: 0.514

Asia WGS AF: 0.648 AC: 2252 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	2.4
DANN	Benign	0.79
PhyloP100		-0.058
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1150893; hg19: chr6-7967946;