rs155502

Variant names:

• chr6-7949573-G-A
• rs155502
• ENST00000439343.2:n.373-44850C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439343.2(BLOC1S5-TXNDC5):​n.373-44850C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,154 control chromosomes in the GnomAD database, including 51,858 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 0.82 (51858 hom., cov: 32)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

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

Verdict is Benign. Variant got -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 = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.423-44850C>T		intron_variant	Intron 4 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLOC1S5-TXNDC5	ENST00000439343.2	n.373-44850C>T		intron_variant	Intron 4 of 12	2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124616 AN: 152036 Hom.: 51806 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.847

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.820 AC: 124717 AN: 152154 Hom.: 51858 Cov.: 32 AF XY: 0.817 AC XY: 60808 AN XY: 74392

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.894

Gnomad4 OTH AF: 0.836

Alfa AF: 0.879 Hom.: 122461

Bravo AF: 0.814

Asia WGS AF: 0.778 AC: 2707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.44

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

Publications

LitVar

Other links and lift over

dbSNP: rs155502; hg19: chr6-7949806;