rs394772

Variant names:

• chr6-28570697-C-T
• rs394772
• NM_052923.2:c.*1214G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052923.2(SCAND3):​c.*1214G>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 0.0516 in 152,138 control chromosomes in the GnomAD database, including 350 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 0.052 (350 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SCAND3 NM_052923.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300
• Publications: 2 publications found

Genes affected

SCAND3 (HGNC:13851): (SCAN domain containing 3) Predicted to enable nucleic acid binding activity. Involved in positive regulation of cell cycle and positive regulation of epithelial cell proliferation. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCAND3	NM_052923.2	c.*1214G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000452236.3	NP_443155.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCAND3	ENST00000452236.3	c.*1214G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_052923.2	ENSP00000395259.2
SCAND3	ENST00000646382.1	c.*1214G>A		3_prime_UTR_variant	Exon 5 of 5			ENSP00000494942.1

Frequencies

GnomAD3 genomes AF: 0.0515 AC: 7823 AN: 152020 Hom.: 344 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0385

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.00378

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0526

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0516 AC: 7851 AN: 152138 Hom.: 350 Cov.: 32 AF XY: 0.0519 AC XY: 3857 AN XY: 74374

African (AFR) AF: 0.128 AC: 5306 AN: 41476

American (AMR) AF: 0.0385 AC: 588 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3468

East Asian (EAS) AF: 0.0666 AC: 345 AN: 5178

South Asian (SAS) AF: 0.0497 AC: 240 AN: 4826

European-Finnish (FIN) AF: 0.00378 AC: 40 AN: 10586

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0165 AC: 1121 AN: 68000

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0303 Hom.: 76

Bravo AF: 0.0580

Asia WGS AF: 0.0640 AC: 222 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		0.030

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs394772; hg19: chr6-28538474;