5-10763544-G-T

Position:

• chr5-10763544-G-T

Variant summary

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

The ENST00000606513.5(DAP-DT):​n.80+2400G>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 0.539 in 152,090 control chromosomes in the GnomAD database, including 24,655 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 0.54 (24655 hom., cov: 34)
• Consequence: DAP-DT ENST00000606513.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

Genes affected

DAP-DT (HGNC:55214): (DAP divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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
DAP-DT	XR_007058693.1	n.97-4080G>T		intron_variant, non_coding_transcript_variant
DAP-DT	XR_002956210.2	n.2068G>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DAP-DT	ENST00000606513.5	n.80+2400G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81897 AN: 151972 Hom.: 24653 Cov.: 34

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.539 AC: 81923 AN: 152090 Hom.: 24655 Cov.: 34 AF XY: 0.529 AC XY: 39311 AN XY: 74358

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.0139

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.532

Alfa AF: 0.502 Hom.: 3039

Bravo AF: 0.523

Asia WGS AF: 0.199 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.78
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4701883; hg19: chr5-10763656;