15-35563921-C-T

Variant summary

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

The NR_038251.1(DPH6-DT):n.279+17448C>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 0.624 in 152,126 control chromosomes in the GnomAD database, including 33,523 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 0.62 (33523 hom., cov: 33)
• Consequence: DPH6-DT NR_038251.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

Genes affected

DPH6-DT (HGNC:44147): (DPH6 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPH6-DT	NR_038251.1	n.279+17448C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPH6-DT	ENST00000501169.3	n.320+17448C>T		intron_variant, non_coding_transcript_variant		1
DPH6-DT	ENST00000559210.1	n.91+17448C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94935 AN: 152008 Hom.: 33521 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.624 AC: 94948 AN: 152126 Hom.: 33523 Cov.: 33 AF XY: 0.634 AC XY: 47164 AN XY: 74370

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.661

Alfa AF: 0.664 Hom.: 5273

Bravo AF: 0.600

Asia WGS AF: 0.761 AC: 2642 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.89
Dann	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs970254; hg19: chr15-35856122;