rs10105

Variant names:

• chr6-25701675-G-A
• rs10105
• NM_006998.4:c.*340G>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.*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
• Publications: 9 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=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGN	NM_006998.4	MANE Select	c.*340G>A		3_prime_UTR	Exon 11 of 11	NP_008929.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGN	ENST00000377961.3	TSL:1 MANE Select	c.*340G>A		3_prime_UTR	Exon 11 of 11	ENSP00000367197.2
	ENSG00000290217	ENST00000703602.1		c.702+10551G>A		intron	N/A	ENSP00000515390.1
	SCGN	ENST00000612225.4	TSL:5	n.*950G>A		non_coding_transcript_exon	Exon 10 of 10	ENSP00000484392.1

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

African (AFR) AF: 0.329 AC: 391 AN: 1190

American (AMR) AF: 0.221 AC: 172 AN: 778

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 431 AN: 1402

East Asian (EAS) AF: 0.0912 AC: 168 AN: 1842

South Asian (SAS) AF: 0.217 AC: 153 AN: 706

European-Finnish (FIN) AF: 0.201 AC: 345 AN: 1720

Middle Eastern (MID) AF: 0.241 AC: 40 AN: 166

European-Non Finnish (NFE) AF: 0.263 AC: 5604 AN: 21342

Other (OTH) AF: 0.244 AC: 573 AN: 2346

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

African (AFR) AF: 0.339 AC: 14060 AN: 41452

American (AMR) AF: 0.247 AC: 3770 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1038 AN: 3468

East Asian (EAS) AF: 0.0927 AC: 478 AN: 5156

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4816

European-Finnish (FIN) AF: 0.204 AC: 2162 AN: 10574

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17964 AN: 67990

Other (OTH) AF: 0.282 AC: 595 AN: 2112

Alfa AF: 0.270 Hom.: 7149

Bravo AF: 0.277

Asia WGS AF: 0.161 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.0
DANN	Benign	0.71
PhyloP100		-0.035
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: rs10105; hg19: chr6-25701903;