rs10245389

Variant names:

• chr7-3901571-T-C
• rs10245389
• NM_152744.4:c.848-49352T>C

Variant summary

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

The NM_152744.4(SDK1):​c.848-49352T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,118 control chromosomes in the GnomAD database, including 5,093 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 0.25 (5093 hom., cov: 32)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 1 publications found

Genes affected

SDK1 (HGNC:19307): (sidekick cell adhesion molecule 1) The protein encoded by this gene is a member of the immunoglobulin superfamily. The protein contains six immunoglobulin-like domains and thirteen fibronectin type III domains. Fibronectin type III domains are present in both extracellular and intracellular proteins and tandem repeats are known to contain binding sites for DNA, heparin and the cell surface. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDK1	NM_152744.4	c.848-49352T>C		intron_variant	Intron 5 of 44	ENST00000404826.7	NP_689957.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDK1	ENST00000404826.7	c.848-49352T>C		intron_variant	Intron 5 of 44	1	NM_152744.4	ENSP00000385899.2
SDK1	ENST00000389531.7	c.848-49352T>C		intron_variant	Intron 5 of 43	5		ENSP00000374182.3

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37361 AN: 152000 Hom.: 5075 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.246 AC: 37430 AN: 152118 Hom.: 5093 Cov.: 32 AF XY: 0.244 AC XY: 18129 AN XY: 74384

African (AFR) AF: 0.351 AC: 14536 AN: 41466

American (AMR) AF: 0.241 AC: 3688 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3470

East Asian (EAS) AF: 0.116 AC: 601 AN: 5172

South Asian (SAS) AF: 0.263 AC: 1264 AN: 4814

European-Finnish (FIN) AF: 0.149 AC: 1576 AN: 10612

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14106 AN: 67990

Other (OTH) AF: 0.260 AC: 548 AN: 2110

Alfa AF: 0.239 Hom.: 975

Bravo AF: 0.255

Asia WGS AF: 0.204 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.67
PhyloP100		0.083
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: rs10245389; hg19: chr7-3941203;