rs2738079

chr8-6959290-C-Achr8-6959290-C-T

Variant summary

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

The NR_073408.1(DEFA9P):n.284G>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 0.124 in 152,262 control chromosomes in the GnomAD database, including 1,425 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 0.12 (1425 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: DEFA9P NR_073408.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

Genes affected

DEFA9P (HGNC:31800): (defensin alpha 9, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DEFA9P	NR_073408.1	n.284G>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DEFA9P	ENST00000433042.1	n.284G>T		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18961 AN: 152140 Hom.: 1426 Cov.: 33

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.134

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.124 AC: 18954 AN: 152258 Hom.: 1425 Cov.: 33 AF XY: 0.127 AC XY: 9457 AN XY: 74448

Gnomad4 AFR AF: 0.0341

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0775 Hom.: 138

Bravo AF: 0.114

Asia WGS AF: 0.225 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.6
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2738079; hg19: chr8-6816812;