rs6976789

chr7-29923318-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_014766.5(SCRN1):c.*639G>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 0.346 in 152,164 control chromosomes in the GnomAD database, including 9,353 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.35 (9340 hom., cov: 32)
  • Exomes 𝑓: 0.39 (13 hom.)
• Consequence: SCRN1 NM_014766.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.20

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 7-29923318-C-T is Benign according to our data. Variant chr7-29923318-C-T is described in ClinVar as [Benign]. Clinvar id is 1257931.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCRN1	NM_014766.5	c.*639G>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.*639G>A		3_prime_UTR_variant	8/8	1	NM_014766.5	P1
SCRN1	ENST00000426154.5	c.*639G>A		3_prime_UTR_variant	8/8	5		P1

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52542 AN: 151912 Hom.: 9320 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.355

GnomAD4 exome AF: 0.386 AC: 51 AN: 132 Hom.: 13 Cov.: 0 AF XY: 0.466 AC XY: 41 AN XY: 88

Gnomad4 AFR exome AF: 0.333

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.402

Gnomad4 OTH exome AF: 0.286

GnomAD4 genome AF: 0.346 AC: 52593 AN: 152032 Hom.: 9340 Cov.: 32 AF XY: 0.345 AC XY: 25642 AN XY: 74300

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.352

Alfa AF: 0.333 Hom.: 11910

Bravo AF: 0.340

Asia WGS AF: 0.268 AC: 934 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 15, 2020

This variant is associated with the following publications: (PMID: 25399950) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.018
Dann	Benign	0.32
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs6976789; hg19: chr7-29962934;