rs10096702

Variant names:

• chr8-18741087-G-A
• rs10096702
• NM_015310.4:c.2172+24362C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-18741087-G-A
• chr8-18741087-G-T

Variant summary

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

The NM_015310.4(PSD3):​c.2172+24362C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 152,234 control chromosomes in the GnomAD database, including 1,120 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 0.091 (1120 hom., cov: 32)
• Consequence: PSD3 NM_015310.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 4 publications found

Genes affected

PSD3 (HGNC:19093): (pleckstrin and Sec7 domain containing 3) Predicted to enable guanyl-nucleotide exchange factor activity and phospholipid binding activity. Predicted to be involved in regulation of ARF protein signal transduction and regulation of catalytic activity. Predicted to be located in membrane. Predicted to be active in ruffle membrane. [provided by Alliance of Genome Resources, Apr 2022]

PSD3 Gene-Disease associations (from GenCC):

• antecubital pterygium syndrome

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

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 (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSD3	NM_015310.4	c.2172+24362C>T		intron_variant	Intron 9 of 15	ENST00000327040.13	NP_056125.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSD3	ENST00000327040.13	c.2172+24362C>T		intron_variant	Intron 9 of 15	1	NM_015310.4	ENSP00000324127.8
PSD3	ENST00000523619.5	c.1977+24362C>T		intron_variant	Intron 8 of 14	1		ENSP00000430640.1
PSD3	ENST00000286485.12	c.570+24362C>T		intron_variant	Intron 6 of 12	1		ENSP00000286485.8
PSD3	ENST00000518315.5	n.*178+24362C>T		intron_variant	Intron 7 of 13	2		ENSP00000428889.1

Frequencies

GnomAD3 genomes AF: 0.0913 AC: 13890 AN: 152116 Hom.: 1115 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0445

Gnomad OTH AF: 0.0928

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

GnomAD4 genome AF: 0.0914 AC: 13909 AN: 152234 Hom.: 1120 Cov.: 32 AF XY: 0.0941 AC XY: 7005 AN XY: 74438

African (AFR) AF: 0.128 AC: 5317 AN: 41520

American (AMR) AF: 0.130 AC: 1996 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 143 AN: 3472

East Asian (EAS) AF: 0.398 AC: 2057 AN: 5164

South Asian (SAS) AF: 0.192 AC: 925 AN: 4824

European-Finnish (FIN) AF: 0.0182 AC: 193 AN: 10622

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0444 AC: 3022 AN: 68018

Other (OTH) AF: 0.0961 AC: 203 AN: 2112

Alfa AF: 0.0622 Hom.: 791

Bravo AF: 0.102

Asia WGS AF: 0.255 AC: 887 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	0.51
DANN	Benign	0.21
PhyloP100		-0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10096702; hg19: chr8-18598597;