chr6-7920575-T-C

Variant names:

• chr6-7920575-T-C
• rs419588
• ENST00000439343.2:n.373-15852A>G

Variant summary

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

The ENST00000439343.2(BLOC1S5-TXNDC5):​n.373-15852A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,164 control chromosomes in the GnomAD database, including 40,148 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 0.71 (40148 hom., cov: 32)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.423-15852A>G		intron_variant	Intron 4 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLOC1S5-TXNDC5	ENST00000439343.2	n.373-15852A>G		intron_variant	Intron 4 of 12	2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108151 AN: 152046 Hom.: 40088 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.711 AC: 108263 AN: 152164 Hom.: 40148 Cov.: 32 AF XY: 0.707 AC XY: 52558 AN XY: 74388

African (AFR) AF: 0.930 AC: 38635 AN: 41550

American (AMR) AF: 0.595 AC: 9101 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2431 AN: 3468

East Asian (EAS) AF: 0.372 AC: 1921 AN: 5164

South Asian (SAS) AF: 0.685 AC: 3298 AN: 4814

European-Finnish (FIN) AF: 0.612 AC: 6483 AN: 10588

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44152 AN: 67984

Other (OTH) AF: 0.694 AC: 1465 AN: 2110

Alfa AF: 0.670 Hom.: 63940

Bravo AF: 0.716

Asia WGS AF: 0.568 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.82
DANN	Benign	0.74
PhyloP100		-1.4
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: rs419588; hg19: chr6-7920808;