6-7917295-T-G

Position:

• chr6-7917295-T-G

Variant summary

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

The ENST00000439343.2(BLOC1S5-TXNDC5):​n.373-12572A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,080 control chromosomes in the GnomAD database, including 3,190 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 0.20 (3190 hom., cov: 32)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

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]

BLOC1S5-TXNDC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.423-12572A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLOC1S5-TXNDC5	ENST00000439343.2	n.373-12572A>C		intron_variant		2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30763 AN: 151962 Hom.: 3187 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.202 AC: 30795 AN: 152080 Hom.: 3190 Cov.: 32 AF XY: 0.202 AC XY: 14981 AN XY: 74336

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.203

Alfa AF: 0.219 Hom.: 4607

Bravo AF: 0.201

Asia WGS AF: 0.200 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.6
DANN	Benign	0.88

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: rs9505309; hg19: chr6-7917528;