rs365936

Variant names:

• chr6-7920671-A-C
• rs365936
• ENST00000439343.2:n.373-15948T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-7920671-A-C
• chr6-7920671-A-G
• chr6-7920671-A-T

Variant summary

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

The ENST00000439343.2(BLOC1S5-TXNDC5):​n.373-15948T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 151,948 control chromosomes in the GnomAD database, including 19,326 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 0.49 (19326 hom., cov: 32)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 9 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.423-15948T>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.373-15948T>G		intron_variant	Intron 4 of 12	2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74932 AN: 151830 Hom.: 19297 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.494 AC: 75019 AN: 151948 Hom.: 19326 Cov.: 32 AF XY: 0.498 AC XY: 36947 AN XY: 74262

African (AFR) AF: 0.641 AC: 26562 AN: 41442

American (AMR) AF: 0.486 AC: 7414 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1150 AN: 3460

East Asian (EAS) AF: 0.438 AC: 2258 AN: 5154

South Asian (SAS) AF: 0.608 AC: 2928 AN: 4814

European-Finnish (FIN) AF: 0.431 AC: 4543 AN: 10538

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28775 AN: 67956

Other (OTH) AF: 0.449 AC: 950 AN: 2114

Alfa AF: 0.435 Hom.: 61977

Bravo AF: 0.495

Asia WGS AF: 0.532 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.87
DANN	Benign	0.43
PhyloP100		-0.0010
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: rs365936; hg19: chr6-7920904;