rs418628

Positions:

• chr6-28585722-C-T

Variant summary

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

The NM_052923.2(SCAND3):​c.420+576G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0511 in 152,230 control chromosomes in the GnomAD database, including 334 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 0.051 (334 hom., cov: 32)
• Consequence: SCAND3 NM_052923.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCAND3	NM_052923.2	c.420+576G>A		intron_variant		ENST00000452236.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCAND3	ENST00000452236.3	c.420+576G>A		intron_variant		1	NM_052923.2	P1
SCAND3	ENST00000646382.1	c.-33-6303G>A		intron_variant
SCAND3	ENST00000526291.1	n.228-401G>A		intron_variant, non_coding_transcript_variant		3
SCAND3	ENST00000530247.1	n.487+1740G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0510 AC: 7754 AN: 152112 Hom.: 329 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0403

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.0495

Gnomad FIN AF: 0.00378

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0169

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0511 AC: 7780 AN: 152230 Hom.: 334 Cov.: 32 AF XY: 0.0512 AC XY: 3808 AN XY: 74418

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0404

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.0666

Gnomad4 SAS AF: 0.0495

Gnomad4 FIN AF: 0.00378

Gnomad4 NFE AF: 0.0169

Gnomad4 OTH AF: 0.0526

Alfa AF: 0.0307 Hom.: 46

Bravo AF: 0.0576

Asia WGS AF: 0.0650 AC: 224 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.50

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: rs418628; hg19: chr6-28553499;