rs73772260

chr5-80151081-G-A

Variant summary

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

The NM_001174072.3(SERINC5):c.987-133C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 698,702 control chromosomes in the GnomAD database, including 13,360 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 0.19 (2847 hom., cov: 33)
  • Exomes 𝑓: 0.19 (10513 hom.)
• Consequence: SERINC5 NM_001174072.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

SERINC5 (HGNC:18825): (serine incorporator 5) Predicted to enable L-serine transmembrane transporter activity. Involved in defense response to virus; detection of virus; and innate immune response. Located in several cellular components, including centrosome; cytosol; and plasma membrane. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SERINC5	NM_001174072.3	c.987-133C>T		intron_variant		ENST00000507668.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SERINC5	ENST00000507668.7	c.987-133C>T		intron_variant		2	NM_001174072.3	P1
SERINC5	ENST00000509193.5	c.987-133C>T		intron_variant		1
SERINC5	ENST00000512972.6	c.987-133C>T		intron_variant, NMD_transcript_variant		2
SERINC5	ENST00000632581.1	c.981-133C>T		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29056 AN: 152024 Hom.: 2843 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0815

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.211

GnomAD4 exome AF: 0.189 AC: 103106 AN: 546560 Hom.: 10513 AF XY: 0.194 AC XY: 56991 AN XY: 294126

Gnomad4 AFR exome AF: 0.199

Gnomad4 AMR exome AF: 0.145

Gnomad4 ASJ exome AF: 0.224

Gnomad4 EAS exome AF: 0.0702

Gnomad4 SAS exome AF: 0.256

Gnomad4 FIN exome AF: 0.152

Gnomad4 NFE exome AF: 0.194

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.191 AC: 29086 AN: 152142 Hom.: 2847 Cov.: 33 AF XY: 0.189 AC XY: 14085 AN XY: 74370

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.0813

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.209

Alfa AF: 0.194 Hom.: 373

Bravo AF: 0.190

Asia WGS AF: 0.166 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.9
Dann	Benign	0.85

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: rs73772260; hg19: chr5-79446904; COSMIC: COSV72597066;