rs139241281

Variant names:

• chr16-21984579-T-C
• rs139241281
• NM_001363519.1:c.483A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-21984579-T-C
• chr16-21984579-T-G

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001363519.1(PDZD9):​c.483A>G​(p.Arg161Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000709 in 1,410,342 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: PDZD9 NM_001363519.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

PDZD9 (HGNC:28740): (PDZ domain containing 9)

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP7: Synonymous conserved (PhyloP=0.062 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDZD9	NM_001363519.1	c.483A>G	p.Arg161Arg	synonymous_variant	Exon 4 of 4	ENST00000424898.3	NP_001350448.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDZD9	ENST00000424898.3	c.483A>G	p.Arg161Arg	synonymous_variant	Exon 4 of 4	5	NM_001363519.1	ENSP00000400514.2
PDZD9	ENST00000523914.5	n.*260A>G		non_coding_transcript_exon_variant	Exon 5 of 5	1		ENSP00000429211.1
PDZD9	ENST00000523914.5	n.*260A>G		3_prime_UTR_variant	Exon 5 of 5	1		ENSP00000429211.1
PDZD9	ENST00000537222.6	c.303A>G	p.Arg101Arg	synonymous_variant	Exon 3 of 3	3		ENSP00000441685.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000440 AC: 1 AN: 227248 Hom.: 0 AF XY: 0.00000814 AC XY: 1 AN XY: 122782

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000938

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 7.09e-7 AC: 1 AN: 1410342 Hom.: 0 Cov.: 30 AF XY: 0.00000144 AC XY: 1 AN XY: 693368

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.24e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs139241281; hg19: chr16-21995900;