chr6-7993744-C-T

Position:

• chr6-7993744-C-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.422+32623G>A 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 0.434 in 151,940 control chromosomes in the GnomAD database, including 15,446 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 0.43 (15446 hom., cov: 31)
• Consequence: BLOC1S5-TXNDC5 NR_037616.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

BLOC1S5-TXNDC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.422+32623G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65891 AN: 151822 Hom.: 15445 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.434 AC: 65930 AN: 151940 Hom.: 15446 Cov.: 31 AF XY: 0.441 AC XY: 32745 AN XY: 74258

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.424

Alfa AF: 0.442 Hom.: 2449

Bravo AF: 0.419

Asia WGS AF: 0.670 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.031
DANN	Benign	0.39

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: rs2567226; hg19: chr6-7993977;