rs17158483

Variant names:

• chr7-29922908-C-T
• rs17158483
• NM_014766.5:c.*1049G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SCRN1	NM_014766.5	c.*1049G>A		3_prime_UTR_variant	Exon 8 of 8	ENST00000242059.10	NP_055581.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCRN1	ENST00000242059.10	c.*1049G>A		3_prime_UTR_variant	Exon 8 of 8	1	NM_014766.5	ENSP00000242059.5
SCRN1	ENST00000426154.5	c.*1049G>A		3_prime_UTR_variant	Exon 8 of 8	5		ENSP00000409068.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0164 AC: 683 AN: 41548

American (AMR) AF: 0.144 AC: 2197 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3472

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5188

South Asian (SAS) AF: 0.0428 AC: 206 AN: 4818

European-Finnish (FIN) AF: 0.0454 AC: 481 AN: 10586

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0769 AC: 5227 AN: 68008

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0778 Hom.: 281

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
PhyloP100		-0.087
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17158483; hg19: chr7-29962524;