chr6-7987650-G-C

Position:

• chr6-7987650-G-C

Variant summary

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

The ENST00000439343.2(BLOC1S5-TXNDC5):​n.372+38717C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 948,782 control chromosomes in the GnomAD database, including 48,777 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 0.38 (12417 hom., cov: 31)
  • Exomes 𝑓: 0.29 (36360 hom.)
• Consequence: BLOC1S5-TXNDC5 ENST00000439343.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIP5K1P1	NR_027712.1	n.1549G>C		non_coding_transcript_exon_variant	1/1
BLOC1S5-TXNDC5	NR_037616.1	n.422+38717C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLOC1S5-TXNDC5	ENST00000439343.2	n.372+38717C>G		intron_variant		2		ENSP00000454697.1
PIP5K1P1	ENST00000460661.1	n.1114G>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57888 AN: 151920 Hom.: 12400 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.399

GnomAD3 exomes AF: 0.309 AC: 77594 AN: 250994 Hom.: 13061 AF XY: 0.305 AC XY: 41442 AN XY: 135660

Gnomad AFR exome AF: 0.579

Gnomad AMR exome AF: 0.315

Gnomad ASJ exome AF: 0.363

Gnomad EAS exome AF: 0.120

Gnomad SAS exome AF: 0.258

Gnomad FIN exome AF: 0.267

Gnomad NFE exome AF: 0.316

Gnomad OTH exome AF: 0.320

GnomAD4 exome AF: 0.291 AC: 231831 AN: 796746 Hom.: 36360 Cov.: 11 AF XY: 0.292 AC XY: 123107 AN XY: 422200

Gnomad4 AFR exome AF: 0.559

Gnomad4 AMR exome AF: 0.319

Gnomad4 ASJ exome AF: 0.358

Gnomad4 EAS exome AF: 0.105

Gnomad4 SAS exome AF: 0.258

Gnomad4 FIN exome AF: 0.262

Gnomad4 NFE exome AF: 0.293

Gnomad4 OTH exome AF: 0.317

GnomAD4 genome AF: 0.381 AC: 57956 AN: 152036 Hom.: 12417 Cov.: 31 AF XY: 0.375 AC XY: 27905 AN XY: 74318

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.400

Alfa AF: 0.262 Hom.: 949

Bravo AF: 0.399

Asia WGS AF: 0.201 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	7.1
DANN	Benign	0.81

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: rs6597293; hg19: chr6-7987883;