rs1074707

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006998.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGN	NM_006998.4	MANE Select	c.472-5782G>A		intron	N/A	NP_008929.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGN	ENST00000377961.3	TSL:1 MANE Select	c.472-5782G>A		intron	N/A	ENSP00000367197.2
	ENSG00000290217	ENST00000703602.1		c.472-5782G>A		intron	N/A	ENSP00000515390.1
	SCGN	ENST00000968674.1		c.472-5782G>A		intron	N/A	ENSP00000638733.1

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

African (AFR) AF: 0.626 AC: 25946 AN: 41430

American (AMR) AF: 0.718 AC: 10984 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2574 AN: 3472

East Asian (EAS) AF: 0.840 AC: 4341 AN: 5170

South Asian (SAS) AF: 0.764 AC: 3678 AN: 4816

European-Finnish (FIN) AF: 0.658 AC: 6942 AN: 10550

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51421 AN: 67962

Other (OTH) AF: 0.720 AC: 1520 AN: 2112

Alfa AF: 0.748 Hom.: 52922

Bravo AF: 0.713

Asia WGS AF: 0.806 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.1
DANN	Benign	0.74
PhyloP100		-0.032
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1074707; hg19: chr6-25676397;