chr11-455008-G-A

Variant names:

• chr11-455008-G-A
• rs11821392
• NM_030783.3:c.182+4371G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030783.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTDSS2	NM_030783.3	MANE Select	c.182+4371G>A		intron	N/A	NP_110410.1
	PTDSS2	NM_001329544.2		c.182+4371G>A		intron	N/A	NP_001316473.1
	PTDSS2	NM_001329548.2		c.3-5179G>A		intron	N/A	NP_001316477.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTDSS2	ENST00000308020.6	TSL:1 MANE Select	c.182+4371G>A		intron	N/A	ENSP00000308258.5
	PTDSS2	ENST00000525059.1	TSL:1	n.393+3515G>A		intron	N/A
	PTDSS2	ENST00000525727.5	TSL:1	n.291+4371G>A		intron	N/A

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

African (AFR) AF: 0.351 AC: 14537 AN: 41408

American (AMR) AF: 0.164 AC: 2502 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3470

East Asian (EAS) AF: 0.183 AC: 944 AN: 5158

South Asian (SAS) AF: 0.199 AC: 959 AN: 4814

European-Finnish (FIN) AF: 0.156 AC: 1653 AN: 10572

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.178 AC: 11975 AN: 67298

Other (OTH) AF: 0.224 AC: 470 AN: 2096

Alfa AF: 0.220 Hom.: 401

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.36
PhyloP100		-1.2
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: rs11821392; hg19: chr11-455008;