6-25653614-T-G

Variant names:

• chr6-25653614-T-G
• rs1406927
• NM_006998.4:c.153+162T>G

Variant summary

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

The NM_006998.4(SCGN):​c.153+162T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,056 control chromosomes in the GnomAD database, including 6,128 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 0.28 (6128 hom., cov: 32)
• Consequence: SCGN NM_006998.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

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=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCGN	NM_006998.4	c.153+162T>G		intron_variant	Intron 2 of 10	ENST00000377961.3	NP_008929.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCGN	ENST00000377961.3	c.153+162T>G		intron_variant	Intron 2 of 10	1	NM_006998.4	ENSP00000367197.2
ENSG00000290217	ENST00000703602.1	c.153+162T>G		intron_variant	Intron 2 of 11			ENSP00000515390.1
SCGN	ENST00000612225.4	n.82+1129T>G		intron_variant	Intron 1 of 9	5		ENSP00000484392.1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42881 AN: 151936 Hom.: 6114 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.282 AC: 42923 AN: 152056 Hom.: 6128 Cov.: 32 AF XY: 0.278 AC XY: 20632 AN XY: 74330

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.275

Alfa AF: 0.281 Hom.: 723

Bravo AF: 0.291

Asia WGS AF: 0.332 AC: 1153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	7.9
DANN	Benign	0.62

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: rs1406927; hg19: chr6-25653842; COSMIC: COSV58544483;