rs17450029

chr1-101075443-T-C

Variant summary

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

The NR_109849.1(DPH5-DT):n.265T>C 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 0.214 in 152,078 control chromosomes in the GnomAD database, including 3,836 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 0.21 (3836 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: DPH5-DT NR_109849.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

Genes affected

DPH5-DT (HGNC:53720): (DPH5 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPH5-DT	NR_109849.1	n.265T>C		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPH5-DT	ENST00000659528.3	n.217-8018T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32520 AN: 151960 Hom.: 3824 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.207

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.214 AC: 32553 AN: 152078 Hom.: 3836 Cov.: 31 AF XY: 0.215 AC XY: 15948 AN XY: 74342

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.206

Alfa AF: 0.237 Hom.: 4208

Bravo AF: 0.216

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.63
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17450029; hg19: chr1-101540999;