rs9857

Variant names:

• chr5-10680435-T-C
• rs9857
• ENST00000230895:c.*621A>G

Variant summary

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

The NM_004394.3(DAP):​c.*621A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 418,666 control chromosomes in the GnomAD database, including 18,649 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 0.31 (7783 hom., cov: 33)
  • Exomes 𝑓: 0.28 (10866 hom.)
• Consequence: DAP NM_004394.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321

Genes affected

DAP (HGNC:2672): (death associated protein) This gene encodes a basic, proline-rich, 15-kD protein. The protein acts as a positive mediator of programmed cell death that is induced by interferon-gamma. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAP	NM_004394.3	c.*621A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000230895.11	NP_004385.1
DAP	NM_001291963.2	c.*272A>G		3_prime_UTR_variant	Exon 3 of 3		NP_001278892.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAP	ENST00000230895	c.*621A>G		3_prime_UTR_variant	Exon 4 of 4	1	NM_004394.3	ENSP00000230895.7
DAP	ENST00000432074.2	c.*272A>G		splice_region_variant	Exon 3 of 3	2		ENSP00000394163.2
DAP	ENST00000432074	c.*272A>G		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000394163.2

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46969 AN: 152004 Hom.: 7765 Cov.: 33

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.311

GnomAD4 exome AF: 0.276 AC: 73444 AN: 266544 Hom.: 10866 Cov.: 0 AF XY: 0.279 AC XY: 38721 AN XY: 139024

Gnomad4 AFR exome AF: 0.397

Gnomad4 AMR exome AF: 0.273

Gnomad4 ASJ exome AF: 0.249

Gnomad4 EAS exome AF: 0.419

Gnomad4 SAS exome AF: 0.335

Gnomad4 FIN exome AF: 0.187

Gnomad4 NFE exome AF: 0.254

Gnomad4 OTH exome AF: 0.277

GnomAD4 genome AF: 0.309 AC: 47019 AN: 152122 Hom.: 7783 Cov.: 33 AF XY: 0.308 AC XY: 22902 AN XY: 74370

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.318

Alfa AF: 0.272 Hom.: 7955

Bravo AF: 0.318

Asia WGS AF: 0.434 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.48
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs9857; hg19: chr5-10680547;