1-31425689-C-T

Position:

• chr1-31425689-C-T

Variant summary

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

The NM_178865.5(SERINC2):​c.473-87C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 1,470,186 control chromosomes in the GnomAD database, including 211,129 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 0.44 (16945 hom., cov: 33)
  • Exomes 𝑓: 0.53 (194184 hom.)
• Consequence: SERINC2 NM_178865.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394

Genes affected

SERINC2 (HGNC:23231): (serine incorporator 2) Predicted to be involved in several processes, including phosphatidylserine metabolic process; positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity; and positive regulation of serine C-palmitoyltransferase activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SERINC2	NM_178865.5	c.473-87C>T		intron_variant		ENST00000373709.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERINC2	ENST00000373709.8	c.473-87C>T		intron_variant		1	NM_178865.5	P1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66941 AN: 151918 Hom.: 16944 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.468

GnomAD4 exome AF: 0.533 AC: 702842 AN: 1318150 Hom.: 194184 AF XY: 0.530 AC XY: 346747 AN XY: 654458

Gnomad4 AFR exome AF: 0.195

Gnomad4 AMR exome AF: 0.462

Gnomad4 ASJ exome AF: 0.561

Gnomad4 EAS exome AF: 0.183

Gnomad4 SAS exome AF: 0.364

Gnomad4 FIN exome AF: 0.538

Gnomad4 NFE exome AF: 0.573

Gnomad4 OTH exome AF: 0.507

GnomAD4 genome AF: 0.440 AC: 66942 AN: 152036 Hom.: 16945 Cov.: 33 AF XY: 0.437 AC XY: 32471 AN XY: 74330

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.465

Alfa AF: 0.501 Hom.: 3118

Bravo AF: 0.427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.6
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2275435; hg19: chr1-31898536; COSMIC: COSV65490231;