rs365936

Positions:

• chr6-7920671-A-C
• chr6-7920671-A-G
• chr6-7920671-A-T

Variant summary

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

The NR_037616.1(BLOC1S5-TXNDC5):​n.423-15948T>G 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 0.494 in 151,948 control chromosomes in the GnomAD database, including 19,326 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 0.49 (19326 hom., cov: 32)
• Consequence: BLOC1S5-TXNDC5 NR_037616.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100

Genes affected

BLOC1S5-TXNDC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.423-15948T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74932 AN: 151830 Hom.: 19297 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.494 AC: 75019 AN: 151948 Hom.: 19326 Cov.: 32 AF XY: 0.498 AC XY: 36947 AN XY: 74262

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.449

Alfa AF: 0.421 Hom.: 29491

Bravo AF: 0.495

Asia WGS AF: 0.532 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.87
DANN	Benign	0.43

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: rs365936; hg19: chr6-7920904;