rs11754300

Variant names:

• chr6-7988533-T-C
• rs11754300
• ENST00000439343.2:n.372+37834A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-7988533-T-C
• chr6-7988533-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.372+37834A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,056 control chromosomes in the GnomAD database, including 1,777 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 0.14 (1777 hom., cov: 31)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 7 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]

PIP5K1P1 (HGNC:28372): (phosphatidylinositol-4-phosphate 5-kinase type 1 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PIP5K1P1	NR_027712.1	n.2432T>C		non_coding_transcript_exon_variant	Exon 1 of 1
BLOC1S5-TXNDC5	NR_037616.1	n.422+37834A>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.372+37834A>G		intron_variant	Intron 4 of 12	2		ENSP00000454697.1

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21498 AN: 151938 Hom.: 1779 Cov.: 31

Gnomad AFR AF: 0.0960

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.141 AC: 21500 AN: 152056 Hom.: 1777 Cov.: 31 AF XY: 0.139 AC XY: 10340 AN XY: 74324

African (AFR) AF: 0.0960 AC: 3984 AN: 41494

American (AMR) AF: 0.108 AC: 1647 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3468

East Asian (EAS) AF: 0.0517 AC: 267 AN: 5160

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4808

European-Finnish (FIN) AF: 0.121 AC: 1277 AN: 10572

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11751 AN: 67968

Other (OTH) AF: 0.154 AC: 324 AN: 2110

Alfa AF: 0.143 Hom.: 292

Bravo AF: 0.134

Asia WGS AF: 0.160 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	15
DANN	Benign	0.79
PhyloP100		-0.032
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: rs11754300; hg19: chr6-7988766;