rs9392182

Positions:

• chr6-8008802-T-A
• chr6-8008802-T-C

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+17565A>T 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 0.74 in 151,920 control chromosomes in the GnomAD database, including 42,718 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 0.74 (42718 hom., cov: 30)
• Consequence: BLOC1S5-TXNDC5 NR_037616.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

Genes affected

BLOC1S5-TXNDC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.422+17565A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112374 AN: 151802 Hom.: 42698 Cov.: 30

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.740 AC: 112438 AN: 151920 Hom.: 42718 Cov.: 30 AF XY: 0.743 AC XY: 55190 AN XY: 74252

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.711

Alfa AF: 0.764 Hom.: 5603

Bravo AF: 0.729

Asia WGS AF: 0.867 AC: 3012 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.69

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: rs9392182; hg19: chr6-8009035;