6-7938540-G-A

Position:

• chr6-7938540-G-A

Variant summary

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

The ENST00000405326.1(ENSG00000217746):​n.783C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,174 control chromosomes in the GnomAD database, including 46,785 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 0.78 (46763 hom., cov: 32)
  • Exomes 𝑓: 0.88 (22 hom.)
• Consequence: ENST00000405326.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BLOC1S5-TXNDC5	NR_037616.1	n.423-33817C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000405326.1	n.783C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118314 AN: 151998 Hom.: 46730 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.799

GnomAD4 exome AF: 0.879 AC: 51 AN: 58 Hom.: 22 Cov.: 0 AF XY: 0.886 AC XY: 39 AN XY: 44

Gnomad4 EAS exome AF: 0.750

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.880

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.778 AC: 118401 AN: 152116 Hom.: 46763 Cov.: 32 AF XY: 0.778 AC XY: 57873 AN XY: 74380

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.801

Alfa AF: 0.832 Hom.: 107232

Bravo AF: 0.769

Asia WGS AF: 0.799 AC: 2777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.60

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: rs155487; hg19: chr6-7938773;