rs1594467

Positions:

• chr6-7920128-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.423-15405T>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 0.36 in 152,138 control chromosomes in the GnomAD database, including 10,244 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 0.36 (10244 hom., cov: 33)
• Consequence: BLOC1S5-TXNDC5 NR_037616.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

Genes affected

BLOC1S5-TXNDC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.423-15405T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54657 AN: 152020 Hom.: 10229 Cov.: 33

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.360 AC: 54707 AN: 152138 Hom.: 10244 Cov.: 33 AF XY: 0.360 AC XY: 26755 AN XY: 74364

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.0860

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.355

Alfa AF: 0.346 Hom.: 10176

Bravo AF: 0.353

Asia WGS AF: 0.277 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.12
DANN	Benign	0.46

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: rs1594467; hg19: chr6-7920361;