rs9406071

Variant names:

• chr6-7974472-C-T
• rs9406071
• ENST00000439343.2:n.372+51895G>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+51895G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,048 control chromosomes in the GnomAD database, including 10,892 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 0.34 (10892 hom., cov: 31)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 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+51895G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLOC1S5-TXNDC5	ENST00000439343.2	TSL:2	n.372+51895G>A		intron	N/A	ENSP00000454697.1	H3BN57

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51510 AN: 151930 Hom.: 10885 Cov.: 31

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.339 AC: 51521 AN: 152048 Hom.: 10892 Cov.: 31 AF XY: 0.346 AC XY: 25721 AN XY: 74304

African (AFR) AF: 0.0835 AC: 3466 AN: 41492

American (AMR) AF: 0.454 AC: 6928 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1162 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3375 AN: 5162

South Asian (SAS) AF: 0.409 AC: 1965 AN: 4810

European-Finnish (FIN) AF: 0.481 AC: 5082 AN: 10562

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28318 AN: 67974

Other (OTH) AF: 0.348 AC: 734 AN: 2110

Alfa AF: 0.376 Hom.: 1934

Bravo AF: 0.328

Asia WGS AF: 0.495 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.72
PhyloP100		-0.66
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: rs9406071; hg19: chr6-7974705;