rs1743634

Variant names:

• chr6-7915974-T-A
• rs1743634
• ENST00000439343.2:n.373-11251A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-7915974-T-A
• chr6-7915974-T-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.373-11251A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 151,936 control chromosomes in the GnomAD database, including 33,927 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 0.67 (33927 hom., cov: 30)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 2 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 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.423-11251A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLOC1S5-TXNDC5	ENST00000439343.2	TSL:2	n.373-11251A>T		intron	N/A	ENSP00000454697.1	H3BN57

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101269 AN: 151818 Hom.: 33888 Cov.: 30

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.667 AC: 101362 AN: 151936 Hom.: 33927 Cov.: 30 AF XY: 0.662 AC XY: 49163 AN XY: 74238

African (AFR) AF: 0.646 AC: 26760 AN: 41408

American (AMR) AF: 0.588 AC: 8985 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2732 AN: 3466

East Asian (EAS) AF: 0.535 AC: 2753 AN: 5144

South Asian (SAS) AF: 0.656 AC: 3148 AN: 4798

European-Finnish (FIN) AF: 0.691 AC: 7303 AN: 10574

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47281 AN: 67950

Other (OTH) AF: 0.689 AC: 1453 AN: 2110

Alfa AF: 0.687 Hom.: 4503

Bravo AF: 0.658

Asia WGS AF: 0.603 AC: 2095 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.68
PhyloP100		-1.3
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1743634;

hg19: chr6-7916207;