rs11514766

Variant names:

• chr7-3900699-C-T
• rs11514766
• NM_152744.4:c.848-50224C>T

Variant summary

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

The NM_152744.4(SDK1):​c.848-50224C>T 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 151,984 control chromosomes in the GnomAD database, including 5,318 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 (5318 hom., cov: 32)
• Consequence: SDK1 NM_152744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 2 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 = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDK1	NM_152744.4	c.848-50224C>T		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.848-50224C>T		intron_variant	Intron 5 of 44	1	NM_152744.4	ENSP00000385899.2
SDK1	ENST00000389531.7	c.848-50224C>T		intron_variant	Intron 5 of 43	5		ENSP00000374182.3

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37362 AN: 151866 Hom.: 5310 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.246 AC: 37416 AN: 151984 Hom.: 5318 Cov.: 32 AF XY: 0.244 AC XY: 18136 AN XY: 74292

African (AFR) AF: 0.390 AC: 16142 AN: 41390

American (AMR) AF: 0.246 AC: 3755 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3468

East Asian (EAS) AF: 0.112 AC: 579 AN: 5170

South Asian (SAS) AF: 0.252 AC: 1210 AN: 4804

European-Finnish (FIN) AF: 0.140 AC: 1483 AN: 10586

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.186 AC: 12622 AN: 67972

Other (OTH) AF: 0.253 AC: 534 AN: 2112

Alfa AF: 0.217 Hom.: 1645

Bravo AF: 0.258

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.54
PhyloP100		-0.013
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: rs11514766; hg19: chr7-3940331;