rs6597292

Positions:

• chr6-7975026-T-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+51341A>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 0.385 in 152,002 control chromosomes in the GnomAD database, including 11,760 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 (11760 hom., cov: 32)
• Consequence: BLOC1S5-TXNDC5 NR_037616.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

BLOC1S5-TXNDC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.422+51341A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58486 AN: 151884 Hom.: 11765 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.385 AC: 58495 AN: 152002 Hom.: 11760 Cov.: 32 AF XY: 0.384 AC XY: 28534 AN XY: 74288

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.398

Alfa AF: 0.370 Hom.: 10935

Bravo AF: 0.384

Asia WGS AF: 0.315 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
DANN	Benign	0.52

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: rs6597292; hg19: chr6-7975259;