rs1074707

Variant names:

• chr6-25676169-G-A
• rs1074707
• NM_006998.4:c.472-5782G>A

Variant summary

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

The NM_006998.4(SCGN):​c.472-5782G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,010 control chromosomes in the GnomAD database, including 38,929 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 0.71 (38929 hom., cov: 31)
• Consequence: SCGN NM_006998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

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]

ENSG00000290217 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCGN	NM_006998.4	c.472-5782G>A		intron_variant	Intron 6 of 10	ENST00000377961.3	NP_008929.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCGN	ENST00000377961.3	c.472-5782G>A		intron_variant	Intron 6 of 10	1	NM_006998.4	ENSP00000367197.2
ENSG00000290217	ENST00000703602.1	c.472-5782G>A		intron_variant	Intron 6 of 11			ENSP00000515390.1
SCGN	ENST00000612225.4	n.*251-5782G>A		intron_variant	Intron 5 of 9	5		ENSP00000484392.1

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108225 AN: 151892 Hom.: 38898 Cov.: 31

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.719

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.712 AC: 108290 AN: 152010 Hom.: 38929 Cov.: 31 AF XY: 0.710 AC XY: 52740 AN XY: 74314

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.720

Alfa AF: 0.747 Hom.: 29180

Bravo AF: 0.713

Asia WGS AF: 0.806 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.1
DANN	Benign	0.74

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: rs1074707; hg19: chr6-25676397;