6-7915974-T-A

Position:

• chr6-7915974-T-A

Variant summary

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

The NR_037616.1(BLOC1S5-TXNDC5):​n.423-11251A>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 0.667 in 151,936 control chromosomes in the GnomAD database, including 33,927 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 0.67 (33927 hom., cov: 30)
• Consequence: BLOC1S5-TXNDC5 NR_037616.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

BLOC1S5-TXNDC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.423-11251A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101269 AN: 151818 Hom.: 33888 Cov.: 30

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.667 AC: 101362 AN: 151936 Hom.: 33927 Cov.: 30 AF XY: 0.662 AC XY: 49163 AN XY: 74238

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.689

Alfa AF: 0.687 Hom.: 4503

Bravo AF: 0.658

Asia WGS AF: 0.603 AC: 2095 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.68

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: rs1743634; hg19: chr6-7916207;