rs10105

chr6-25701675-G-A

Variant summary

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

The NM_006998.4(SCGN):c.*340G>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 0.269 in 183,544 control chromosomes in the GnomAD database, including 6,991 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 0.27 (5931 hom., cov: 32)
  • Exomes 𝑓: 0.25 (1060 hom.)
• Consequence: SCGN NM_006998.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

SCGN (HGNC:16941): (secretagogin, EF-hand calcium binding protein) The encoded protein is a secreted calcium-binding protein which is found in the cytoplasm. It is related to calbindin D-28K and calretinin. This protein is thought to be involved in KCL-stimulated calcium flux and cell proliferation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCGN	NM_006998.4	c.*340G>A		3_prime_UTR_variant	11/11	ENST00000377961.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCGN	ENST00000377961.3	c.*340G>A		3_prime_UTR_variant	11/11	1	NM_006998.4	P1
SCGN	ENST00000612225.4	c.*950G>A		3_prime_UTR_variant, NMD_transcript_variant	10/10	5

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41401 AN: 151934 Hom.: 5922 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0927

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.286

GnomAD4 exome AF: 0.250 AC: 7877 AN: 31492 Hom.: 1060 Cov.: 0 AF XY: 0.254 AC XY: 3981 AN XY: 15662

Gnomad4 AFR exome AF: 0.329

Gnomad4 AMR exome AF: 0.221

Gnomad4 ASJ exome AF: 0.307

Gnomad4 EAS exome AF: 0.0912

Gnomad4 SAS exome AF: 0.217

Gnomad4 FIN exome AF: 0.201

Gnomad4 NFE exome AF: 0.263

Gnomad4 OTH exome AF: 0.244

GnomAD4 genome AF: 0.272 AC: 41414 AN: 152052 Hom.: 5931 Cov.: 32 AF XY: 0.268 AC XY: 19900 AN XY: 74318

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.0927

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.282

Alfa AF: 0.268 Hom.: 5526

Bravo AF: 0.277

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	4.0
Dann	Benign	0.71

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: rs10105; hg19: chr6-25701903;