ENST00000439343.2:n.372+53220T>C

Variant names:

• chr6-7973147-A-G
• rs7763447
• ENST00000439343.2:n.372+53220T>C

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+53220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,962 control chromosomes in the GnomAD database, including 19,108 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 0.49 (19108 hom., cov: 31)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 3 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439343.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLOC1S5-TXNDC5	NR_037616.1		n.422+53220T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLOC1S5-TXNDC5	ENST00000439343.2	TSL:2	n.372+53220T>C		intron	N/A	ENSP00000454697.1	H3BN57

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75028 AN: 151846 Hom.: 19090 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.494 AC: 75089 AN: 151962 Hom.: 19108 Cov.: 31 AF XY: 0.486 AC XY: 36077 AN XY: 74278

African (AFR) AF: 0.576 AC: 23843 AN: 41420

American (AMR) AF: 0.430 AC: 6556 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2055 AN: 3466

East Asian (EAS) AF: 0.182 AC: 941 AN: 5180

South Asian (SAS) AF: 0.488 AC: 2346 AN: 4806

European-Finnish (FIN) AF: 0.380 AC: 4014 AN: 10566

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.494 AC: 33550 AN: 67950

Other (OTH) AF: 0.527 AC: 1111 AN: 2108

Alfa AF: 0.504 Hom.: 19225

Bravo AF: 0.500

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		-1.7
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: rs7763447; hg19: chr6-7973380;