rs11821392

Positions:

• chr11-455008-G-A

Variant summary

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

The NM_030783.3(PTDSS2):​c.182+4371G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 151,232 control chromosomes in the GnomAD database, including 4,338 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 0.22 (4338 hom., cov: 32)
• Consequence: PTDSS2 NM_030783.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

PTDSS2 (HGNC:15463): (phosphatidylserine synthase 2) The protein encoded by this gene catalyzes the conversion of phosphatidylethanolamine to phosphatidylserine, a structural membrane phospholipid that functions in cell signaling, blood coagulation, and apoptosis. The encoded enzyme also has a high affinity for docosahexaenoic acid (DHA) and can use it to make DHA-containing phosphatidylserine. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTDSS2	NM_030783.3	c.182+4371G>A		intron_variant		ENST00000308020.6	NP_110410.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTDSS2	ENST00000308020.6	c.182+4371G>A		intron_variant		1	NM_030783.3	ENSP00000308258	P1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34000 AN: 151114 Hom.: 4328 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.225 AC: 34023 AN: 151232 Hom.: 4338 Cov.: 32 AF XY: 0.223 AC XY: 16487 AN XY: 73926

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.224

Alfa AF: 0.213 Hom.: 363

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.36

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: rs11821392; hg19: chr11-455008;