rs17158483

chr7-29922908-C-T

Variant summary

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

The NM_014766.5(SCRN1):c.*1049G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0591 in 152,244 control chromosomes in the GnomAD database, including 423 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 0.059 (423 hom., cov: 33)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: SCRN1 NM_014766.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

Genes affected

SCRN1 (HGNC:22192): (secernin 1) This gene likely encodes a member of the secernin family of proteins. A similar protein in rat functions in regulation of exocytosis in mast cells. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCRN1	NM_014766.5	c.*1049G>A		3_prime_UTR_variant	8/8	ENST00000242059.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCRN1	ENST00000242059.10	c.*1049G>A		3_prime_UTR_variant	8/8	1	NM_014766.5	P1
SCRN1	ENST00000426154.5	c.*1049G>A		3_prime_UTR_variant	8/8	5		P1

Frequencies

GnomAD3 genomes AF: 0.0592 AC: 9007 AN: 152118 Hom.: 424 Cov.: 33

Gnomad AFR AF: 0.0165

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.0454

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.0526

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.0591 AC: 9001 AN: 152236 Hom.: 423 Cov.: 33 AF XY: 0.0586 AC XY: 4359 AN XY: 74424

Gnomad4 AFR AF: 0.0164

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0153

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0428

Gnomad4 FIN AF: 0.0454

Gnomad4 NFE AF: 0.0769

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0797 Hom.: 260

Bravo AF: 0.0649

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	11
Dann	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs17158483; hg19: chr7-29962524;