8-6959290-C-A

Variant names:

• chr8-6959290-C-A
• rs2738079
• ENST00000433042.1:n.284G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000433042.1(DEFA9P):​n.284G>T variant causes a splice region, 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 ENST00000433042.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DEFA9P	NR_073408.1	n.284G>T		splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DEFA9P	ENST00000433042.1	n.284G>T		splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 2	6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.0341 AC: 1416 AN: 41558

American (AMR) AF: 0.106 AC: 1628 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3470

East Asian (EAS) AF: 0.182 AC: 941 AN: 5180

South Asian (SAS) AF: 0.222 AC: 1073 AN: 4830

European-Finnish (FIN) AF: 0.157 AC: 1660 AN: 10590

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.164 AC: 11185 AN: 68016

Other (OTH) AF: 0.136 AC: 287 AN: 2112

Alfa AF: 0.0764 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
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs2738079; hg19: chr8-6816812;