rs6104890

Variant names:

• chr20-1311725-C-T
• rs6104890
• NM_080489.5:c.732+612G>A

Variant summary

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

The NM_080489.5(SDCBP2):​c.732+612G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,078 control chromosomes in the GnomAD database, including 42,378 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 0.74 (42378 hom., cov: 31)
• Consequence: SDCBP2 NM_080489.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 1 publications found

Genes affected

SDCBP2 (HGNC:15756): (syndecan binding protein 2) The protein encoded by this gene contains two class II PDZ domains. PDZ domains facilitate protein-protein interactions by binding to the cytoplasmic C-terminus of transmembrane proteins, and PDZ-containing proteins mediate cell signaling and the organization of protein complexes. The encoded protein binds to phosphatidylinositol 4, 5-bisphosphate (PIP2) and plays a role in nuclear PIP2 organization and cell division. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Read-through transcription also exists between this gene and the upstream FKBP1A (FK506 binding protein 1A, 12kDa) gene, as represented in GeneID:100528031. [provided by RefSeq, Sep 2011]

FKBP1A-SDCBP2 (HGNC:41997): (FKBP1A-SDCBP2 readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring FK506 binding protein 1A, 12kDa and syndecan binding protein (syntenin) 2 genes on chromosome 20. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is unlikely to produce a protein product. [provided by RefSeq, Dec 2010]

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 (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDCBP2	NM_080489.5	c.732+612G>A		intron_variant	Intron 7 of 8	ENST00000360779.4	NP_536737.3
SDCBP2	NM_001199784.2	c.732+612G>A		intron_variant	Intron 7 of 8		NP_001186713.1
SDCBP2	NM_015685.6	c.477+612G>A		intron_variant	Intron 3 of 4		NP_056500.2
FKBP1A-SDCBP2	NR_037661.1	n.1010+612G>A		intron_variant	Intron 8 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDCBP2	ENST00000360779.4	c.732+612G>A		intron_variant	Intron 7 of 8	1	NM_080489.5	ENSP00000354013.3
SDCBP2	ENST00000339987.7	c.732+612G>A		intron_variant	Intron 7 of 8	1		ENSP00000342935.3
SDCBP2	ENST00000381808.7	c.477+612G>A		intron_variant	Intron 3 of 4	1		ENSP00000371229.3
SDCBP2	ENST00000381812.5	c.732+612G>A		intron_variant	Intron 7 of 8	5		ENSP00000371233.1

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112473 AN: 151960 Hom.: 42367 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.740 AC: 112518 AN: 152078 Hom.: 42378 Cov.: 31 AF XY: 0.747 AC XY: 55541 AN XY: 74346

African (AFR) AF: 0.584 AC: 24194 AN: 41436

American (AMR) AF: 0.795 AC: 12151 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2398 AN: 3470

East Asian (EAS) AF: 0.922 AC: 4767 AN: 5172

South Asian (SAS) AF: 0.819 AC: 3947 AN: 4820

European-Finnish (FIN) AF: 0.863 AC: 9134 AN: 10578

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53475 AN: 68000

Other (OTH) AF: 0.735 AC: 1550 AN: 2110

Alfa AF: 0.753 Hom.: 5642

Bravo AF: 0.726

Asia WGS AF: 0.843 AC: 2932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.76
PhyloP100		-0.018
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: rs6104890; hg19: chr20-1292369;