rs9328448

chr6-8000884-A-G

Variant summary

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

The NR_037616.1(BLOC1S5-TXNDC5):n.422+25483T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,222 control chromosomes in the GnomAD database, including 3,049 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 0.19 (3049 hom., cov: 32)
• Consequence: BLOC1S5-TXNDC5 NR_037616.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580

Genes affected

BLOC1S5-TXNDC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.422+25483T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29318 AN: 152104 Hom.: 3044 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0769

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.193 AC: 29359 AN: 152222 Hom.: 3049 Cov.: 32 AF XY: 0.189 AC XY: 14055 AN XY: 74440

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0768

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.181

Gnomad4 OTH AF: 0.188

Alfa AF: 0.183 Hom.: 3476

Bravo AF: 0.202

Asia WGS AF: 0.100 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	16
Dann	Benign	0.75

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: rs9328448; hg19: chr6-8001117;